Source Code for Module test_suite.system_tests.relax_disp

   1  ############################################################################### 
   2  #                                                                             # 
   3  # Copyright (C) 2006-2014 Edward d'Auvergne                                   # 
   4  # Copyright (C) 2009 Sebastien Morin                                          # 
   5  # Copyright (C) 2013-2014 Troels E. Linnet                                    # 
   6  #                                                                             # 
   7  # This file is part of the program relax (http://www.nmr-relax.com).          # 
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   9  # This program is free software: you can redistribute it and/or modify        # 
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  15  # but WITHOUT ANY WARRANTY; without even the implied warranty of              # 
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  17  # GNU General Public License for more details.                                # 
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  20  # along with this program.  If not, see <http://www.gnu.org/licenses/>.       # 
  21  #                                                                             # 
  22  ############################################################################### 
  23   
  24  # Python module imports. 
  25  from os import F_OK, access, getcwd, path, sep 
  26  from numpy import array, asarray, exp, median, inf, log, save, std, sum, zeros 
  27  from minfx.generic import generic_minimise 
  28  from random import gauss 
  29  import re, math 
  30  from tempfile import mkdtemp, NamedTemporaryFile 
  31   
  32   
  33  # relax module imports. 
  34  from auto_analyses import relax_disp 
  35  from data_store import Relax_data_store; ds = Relax_data_store() 
  36  import dep_check 
  37  from lib.errors import RelaxError 
  38  from lib.io import get_file_path 
  39  from pipe_control.mol_res_spin import generate_spin_string, return_spin, spin_loop 
  40  from pipe_control.minimise import assemble_scaling_matrix 
  41  from specific_analyses.relax_disp.checks import check_missing_r1 
  42  from specific_analyses.relax_disp.estimate_r2eff import estimate_r2eff 
  43  from specific_analyses.relax_disp.data import average_intensity, check_intensity_errors, generate_r20_key, get_curve_type, has_exponential_exp_type, has_r1rho_exp_type, loop_exp_frq, loop_exp_frq_offset_point, loop_exp_frq_offset_point_time, loop_time, return_grace_file_name_ini, return_param_key_from_data, spin_ids_to_containers 
  44  from specific_analyses.relax_disp.data import INTERPOLATE_DISP, INTERPOLATE_OFFSET, X_AXIS_DISP, X_AXIS_W_EFF, X_AXIS_THETA, Y_AXIS_R2_R1RHO, Y_AXIS_R2_EFF 
  45  from specific_analyses.relax_disp.model import models_info, nesting_param 
  46  from specific_analyses.relax_disp.parameters import linear_constraints 
  47  from specific_analyses.relax_disp.variables import EXP_TYPE_CPMG_DQ, EXP_TYPE_CPMG_MQ, EXP_TYPE_CPMG_PROTON_MQ, EXP_TYPE_CPMG_PROTON_SQ, EXP_TYPE_CPMG_SQ, EXP_TYPE_CPMG_ZQ, EXP_TYPE_LIST, EXP_TYPE_R1RHO, MODEL_B14_FULL, MODEL_CR72, MODEL_CR72_FULL, MODEL_DPL94, MODEL_IT99, MODEL_LIST_ANALYTIC_CPMG, MODEL_LIST_FULL, MODEL_LIST_NUMERIC_CPMG, MODEL_LM63, MODEL_M61, MODEL_M61B, MODEL_MP05, MODEL_NOREX, MODEL_NS_CPMG_2SITE_3D_FULL, MODEL_NS_CPMG_2SITE_EXPANDED, MODEL_NS_CPMG_2SITE_STAR_FULL, MODEL_NS_R1RHO_2SITE, MODEL_NS_R1RHO_3SITE, MODEL_NS_R1RHO_3SITE_LINEAR, MODEL_PARAMS, MODEL_R2EFF, MODEL_TP02, MODEL_TAP03 
  48  from status import Status; status = Status() 
  49  from test_suite.system_tests.base_classes import SystemTestCase 
  50   
  51  # C modules. 
  52  if dep_check.C_module_exp_fn: 
  53      from specific_analyses.relax_fit.optimisation import func_wrapper, dfunc_wrapper, d2func_wrapper 
  54      from target_functions.relax_fit import jacobian, jacobian_chi2, setup 
  55      # Call the python wrapper function to help with list to numpy array conversion. 
  56      func = func_wrapper 
  57      dfunc = dfunc_wrapper 
  58      d2func = d2func_wrapper 
  59   
  60   
  61 -class Relax_disp(SystemTestCase): 
  62      """Class for testing various aspects specific to relaxation dispersion curve-fitting.""" 
  63   
  64 -    def __init__(self, methodName='runTest'): 
  65          """Skip certain tests if the C modules are non-functional. 
  66   
  67          @keyword methodName:    The name of the test. 
  68          @type methodName:       str 
  69          """ 
  70   
  71          # Execute the base class method. 
  72          super(Relax_disp, self).__init__(methodName) 
  73   
  74          # Missing module. 
  75          if not dep_check.C_module_exp_fn: 
  76              # The list of tests to skip. 
  77              to_skip = [ 
  78                  "test_bug_atul_srivastava", 
  79                  "test_bug_21344_sparse_time_spinlock_acquired_r1rho_fail_relax_disp", 
  80                  "test_bug_9999_slow_r1rho_r2eff_error_with_mc", 
  81                  "test_estimate_r2eff_err", 
  82                  "test_estimate_r2eff_err_auto", 
  83                  "test_estimate_r2eff_err_methods", 
  84                  "test_finite_value", 
  85                  "test_exp_fit", 
  86                  "test_m61_exp_data_to_m61", 
  87                  "test_r1rho_kjaergaard_auto", 
  88                  "test_r1rho_kjaergaard_auto_check_graphs", 
  89                  "test_r1rho_kjaergaard_man", 
  90                  "test_r1rho_kjaergaard_missing_r1", 
  91                  "test_value_write_calc_rotating_frame_params_auto_analysis" 
  92              ] 
  93   
  94              # Store in the status object. 
  95              if methodName in to_skip: 
  96                  status.skipped_tests.append([methodName, 'Relax curve-fitting C module', self._skip_type]) 
  97   
  98          # If not scipy.optimize.leastsq. 
  99          if not dep_check.scipy_module: 
 100              # The list of tests to skip. 
 101              to_skip = [ 
 102                  "test_estimate_r2eff_err_methods" 
 103              ] 
 104   
 105              # Store in the status object. 
 106              if methodName in to_skip: 
 107                  status.skipped_tests.append([methodName, 'scipy.optimize.leastsq module', self._skip_type]) 
 108   
 109   
 110 -    def setUp(self): 
 111          """Set up for all the functional tests.""" 
 112   
 113          # Create the data pipe. 
 114          self.interpreter.pipe.create('relax_disp', 'relax_disp') 
 115   
 116          # Create a temporary directory for dumping files. 
 117          ds.tmpdir = mkdtemp() 
 118          self.tmpdir = ds.tmpdir 
 119   
 120   
 121 -    def setup_bug_22146_unpacking_r2a_r2b_cluster(self, folder=None, model_analyse=None, places = 7): 
 122          """Setup data for the catch of U{bug #22146<https://gna.org/bugs/?22146>}, the failure of unpacking R2A and R2B, when performing a clustered full dispersion models. 
 123   
 124          @keyword folder:            The name of the folder for the test data. 
 125          @type folder:               str 
 126          @keyword model_analyse:     The name of the model which will be tested. 
 127          @type model_analyse:        str 
 128          """ 
 129   
 130          data_path = status.install_path + sep+'test_suite'+sep+'shared_data'+sep+'dispersion'+sep+'Hansen' 
 131   
 132          # Data. 
 133          data_path = status.install_path + sep+'test_suite'+sep+'shared_data'+sep+'dispersion'+sep+'bug_22146_unpacking_r2a_r2b_cluster'+sep+folder 
 134   
 135          ## Experiments 
 136          # Exp 1 
 137          sfrq_1 = 500.0*1E6 
 138          r20_key_1 = generate_r20_key(exp_type=EXP_TYPE_CPMG_SQ, frq=sfrq_1) 
 139          time_T2_1 = 0.05 
 140          ncycs_1 = [2, 4, 6, 8, 10, 12, 14, 16, 18, 20, 40, 50] 
 141          # Here you define the direct R2eff errors (rad/s), as being added or subtracted for the created R2eff point in the corresponding ncyc cpmg frequence. 
 142          #r2eff_errs_1 = [0.05, -0.05, 0.05, -0.05, 0.05, -0.05, 0.05, -0.05, 0.05, -0.05, 0.05, -0.05, 0.05, -0.05, 0.05] 
 143          r2eff_errs_1 = [0.0] * len(ncycs_1) 
 144          exp_1 = [sfrq_1, time_T2_1, ncycs_1, r2eff_errs_1] 
 145   
 146          sfrq_2 = 600.0*1E6 
 147          r20_key_2 = generate_r20_key(exp_type=EXP_TYPE_CPMG_SQ, frq=sfrq_2) 
 148          time_T2_2 = 0.06 
 149          ncycs_2 = [2, 4, 6, 8, 10, 12, 14, 16, 18, 20, 40, 60] 
 150          # Here you define the direct R2eff errors (rad/s), as being added or subtracted for the created R2eff point in the corresponding ncyc cpmg frequence. 
 151          #r2eff_errs_2 = [0.05, -0.05, 0.05, -0.05, 0.05, -0.05, 0.05, -0.05, 0.05, -0.05, 0.05, -0.05, 0.05, -0.05, 0.05, -0.05, 0.05] 
 152          r2eff_errs_2 = [0.0] * len(ncycs_2) 
 153          exp_2 = [sfrq_2, time_T2_2, ncycs_2, r2eff_errs_2] 
 154   
 155          sfrq_3 = 700.0*1E6 
 156          r20_key_3 = generate_r20_key(exp_type=EXP_TYPE_CPMG_SQ, frq=sfrq_3) 
 157          time_T2_3 = 0.07 
 158          ncycs_3 = [2, 4, 6, 8, 10, 12, 14, 16, 18, 20, 50, 70] 
 159          # Here you define the direct R2eff errors (rad/s), as being added or subtracted for the created R2eff point in the corresponding ncyc cpmg frequence. 
 160          #r2eff_errs_2 = [0.05, -0.05, 0.05, -0.05, 0.05, -0.05, 0.05, -0.05, 0.05, -0.05, 0.05, -0.05, 0.05, -0.05, 0.05, -0.05, 0.05] 
 161          r2eff_errs_3 = [0.0] * len(ncycs_3) 
 162          exp_3 = [sfrq_3, time_T2_3, ncycs_3, r2eff_errs_3] 
 163   
 164          # Collect all exps 
 165          exps = [exp_1, exp_2, exp_3] 
 166   
 167          R20 = [5.1, 5.2, 5.3, 10.1, 10.2, 10.3, 6.1, 6.2, 6.3, 11.1, 11.2, 11.3, 7.1, 7.2, 7.3, 12.1, 12.2, 12.3, 8.1, 8.2, 8.3, 13.1, 13.2, 13.3] 
 168          dw_arr = [1.0, 2.0, 3.0, 4.0] 
 169          pA_arr = [0.9] 
 170          kex_arr = [1000.] 
 171   
 172          spins = [ 
 173                  ['Ala', 1, 'N', {'r2a': {r20_key_1: R20[0], r20_key_2: R20[1], r20_key_3: R20[2]}, 'r2b': {r20_key_1: R20[3], r20_key_2: R20[4], r20_key_3: R20[5]}, 'kex': kex_arr[0], 'pA': pA_arr[0], 'dw': dw_arr[0]}], 
 174                  ['Ala', 2, 'N', {'r2a': {r20_key_1: R20[6], r20_key_2: R20[7], r20_key_3: R20[8]}, 'r2b': {r20_key_1: R20[9], r20_key_2: R20[10], r20_key_3: R20[11]}, 'kex': kex_arr[0], 'pA': pA_arr[0], 'dw': dw_arr[1]}], 
 175                  ['Ala', 3, 'N', {'r2a': {r20_key_1: R20[12], r20_key_2: R20[13], r20_key_3: R20[14]}, 'r2b': {r20_key_1: R20[15], r20_key_2: R20[16], r20_key_3: R20[17]}, 'kex': kex_arr[0], 'pA': pA_arr[0], 'dw': dw_arr[2]}], 
 176                  ['Ala', 4, 'N', {'r2a': {r20_key_1: R20[18], r20_key_2: R20[19], r20_key_3: R20[20]}, 'r2b': {r20_key_1: R20[21], r20_key_2: R20[22], r20_key_3: R20[23]}, 'kex': kex_arr[0], 'pA': pA_arr[0], 'dw': dw_arr[3]}], 
 177                  ] 
 178   
 179          # Create the data pipe. 
 180          pipe_name = 'base pipe' 
 181          pipe_type = 'relax_disp' 
 182          pipe_bundle = 'relax_disp' 
 183          self.interpreter.pipe.create(pipe_name=pipe_name, pipe_type=pipe_type, bundle = pipe_bundle) 
 184   
 185          # Generate the sequence. 
 186          for res_name, res_num, spin_name, params in spins: 
 187              self.interpreter.spin.create(res_name=res_name, res_num=res_num, spin_name=spin_name) 
 188   
 189          # Set isotope 
 190          self.interpreter.spin.isotope('15N', spin_id='@N') 
 191   
 192          # Now loop over the experiments, to set the variables in relax. 
 193          exp_ids = [] 
 194          for exp_i in exps: 
 195              sfrq, time_T2, ncycs, r2eff_errs = exp_i 
 196              exp_id = 'CPMG_%3.1f' % (sfrq/1E6) 
 197              exp_ids.append(exp_id) 
 198   
 199              ids = [] 
 200              for ncyc in ncycs: 
 201                  nu_cpmg = ncyc / time_T2 
 202                  cur_id = '%s_%.1f' % (exp_id, nu_cpmg) 
 203                  ids.append(cur_id) 
 204   
 205                  # Set the spectrometer frequency. 
 206                  self.interpreter.spectrometer.frequency(id=cur_id, frq=sfrq) 
 207   
 208                  # Set the experiment type. 
 209                  self.interpreter.relax_disp.exp_type(spectrum_id=cur_id, exp_type=EXP_TYPE_CPMG_SQ) 
 210   
 211                  # Set the relaxation dispersion CPMG constant time delay T (in s). 
 212                  self.interpreter.relax_disp.relax_time(spectrum_id=cur_id, time=time_T2) 
 213   
 214                  # Set the relaxation dispersion CPMG frequencies. 
 215                  self.interpreter.relax_disp.cpmg_setup(spectrum_id=cur_id, cpmg_frq=nu_cpmg) 
 216   
 217          print("\n\nThe experiment IDs are %s." % cdp.spectrum_ids) 
 218   
 219          ### Now do fitting. 
 220          # Change pipe. 
 221   
 222          pipe_name_MODEL = "%s_%s"%(pipe_name, model_analyse) 
 223          self.interpreter.pipe.copy(pipe_from=pipe_name, pipe_to=pipe_name_MODEL, bundle_to = pipe_bundle) 
 224          self.interpreter.pipe.switch(pipe_name=pipe_name_MODEL) 
 225   
 226          # Now read data in. 
 227          for exp_type, frq, ei, mi in loop_exp_frq(return_indices=True): 
 228              exp_id = exp_ids[mi] 
 229              exp_i = exps[mi] 
 230              sfrq, time_T2, ncycs, r2eff_errs = exp_i 
 231   
 232              # Then loop over the spins. 
 233              for res_name, res_num, spin_name, params in spins: 
 234                  cur_spin_id = ":%i@%s"%(res_num, spin_name) 
 235   
 236                  # Define file name 
 237                  file_name = "%s%s.txt" % (exp_id, cur_spin_id .replace('#', '_').replace(':', '_').replace('@', '_')) 
 238   
 239                  # Read in the R2eff file to put into spin structure. 
 240                  self.interpreter.relax_disp.r2eff_read_spin(id=exp_id, spin_id=cur_spin_id, file=file_name, dir=data_path, disp_point_col=1, data_col=2, error_col=3) 
 241   
 242          # Then select model. 
 243          self.interpreter.relax_disp.select_model(model=model_analyse) 
 244   
 245          # Then cluster 
 246          self.interpreter.relax_disp.cluster('model_cluster', ":1-100") 
 247   
 248          # Grid search 
 249          low_arr = R20 + dw_arr + pA_arr + kex_arr 
 250          self.interpreter.minimise.grid_search(lower=low_arr, upper=low_arr, inc=1, constraints=True, verbosity=1) 
 251   
 252          # Then loop over the defined spins and read the parameters. 
 253          for i in range(len(spins)): 
 254              res_name, res_num, spin_name, params = spins[i] 
 255              cur_spin_id = ":%i@%s"%(res_num, spin_name) 
 256              cur_spin = return_spin(cur_spin_id) 
 257   
 258              for mo_param in cur_spin.params: 
 259                  print(mo_param) 
 260                  # The R2 is a dictionary, depending on spectrometer frequency. 
 261                  if isinstance(getattr(cur_spin, mo_param), dict): 
 262                      for key, val in getattr(cur_spin, mo_param).items(): 
 263                          should_be = params[mo_param][key] 
 264                          print(cur_spin.model, res_name, cur_spin_id, mo_param, key, float(val), should_be) 
 265                          self.assertAlmostEqual(val, should_be) 
 266                  else: 
 267                      should_be = float(params[mo_param]) 
 268                      val = getattr(cur_spin, mo_param) 
 269                      print(cur_spin.model, res_name, cur_spin_id, mo_param, val, should_be) 
 270                      self.assertAlmostEqual(val, should_be) 
 271   
 272              # Test chi2. 
 273              # At this point the chi-squared value at the solution should be zero, as the relaxation data was created with the same parameter values. 
 274              self.assertAlmostEqual(cur_spin.chi2, 0.0, places = places) 
 275   
 276   
 277 -    def setup_r1rho_kjaergaard(self, cluster_ids=[], read_R1=True): 
 278          """Set up the data for the test_r1rho_kjaergaard_*() system tests.""" 
 279   
 280          # The path to the data files. 
 281          data_path = status.install_path + sep+'test_suite'+sep+'shared_data'+sep+'dispersion'+sep+'Kjaergaard_et_al_2013' 
 282   
 283          # Set pipe name, bundle and type. 
 284          ds.pipe_name = 'base pipe' 
 285          ds.pipe_bundle = 'relax_disp' 
 286          ds.pipe_type = 'relax_disp' 
 287   
 288          # Create the data pipe. 
 289          self.interpreter.pipe.create(pipe_name=ds.pipe_name, bundle=ds.pipe_bundle, pipe_type=ds.pipe_type) 
 290   
 291          # Read the spins. 
 292          self.interpreter.spectrum.read_spins(file='1_0_46_0_max_standard.ser', dir=data_path+sep+'peak_lists') 
 293   
 294          # Name the isotope for field strength scaling. 
 295          self.interpreter.spin.isotope(isotope='15N') 
 296   
 297          # Set number of experiments to be used. 
 298          NR_exp = 70 
 299   
 300          # Load the experiments settings file. 
 301          expfile = open(data_path+sep+'exp_parameters_sort.txt', 'r') 
 302          expfileslines = expfile.readlines()[:NR_exp] 
 303          expfile.close() 
 304   
 305          # In MHz 
 306          yOBS = 81.050 
 307          # In ppm 
 308          yCAR = 118.078 
 309          centerPPM_N15 = yCAR 
 310   
 311          ## Read the chemical shift data. 
 312          self.interpreter.chemical_shift.read(file='1_0_46_0_max_standard.ser', dir=data_path+sep+'peak_lists') 
 313   
 314          # The lock power to field, has been found in an calibration experiment. 
 315          spin_lock_field_strengths_Hz = {'35': 431.0, '39': 651.2, '41': 800.5, '43': 984.0, '46': 1341.11, '48': 1648.5} 
 316   
 317          # Apply spectra settings. 
 318          # Count settings 
 319          j = 0 
 320          for i in range(len(expfileslines)): 
 321              line = expfileslines[i] 
 322              if line[0] == "#": 
 323                  continue 
 324              else: 
 325                  # DIRN I deltadof2 dpwr2slock ncyc trim ss sfrq 
 326                  DIRN = line.split()[0] 
 327                  I = int(line.split()[1]) 
 328                  deltadof2 = line.split()[2] 
 329                  dpwr2slock = line.split()[3] 
 330                  ncyc = int(line.split()[4]) 
 331                  trim = float(line.split()[5]) 
 332                  ss = int(line.split()[6]) 
 333                  set_sfrq = float(line.split()[7]) 
 334                  apod_rmsd = float(line.split()[8]) 
 335                  spin_lock_field_strength = spin_lock_field_strengths_Hz[dpwr2slock] 
 336   
 337                  # Calculate spin_lock time 
 338                  time_sl = 2*ncyc*trim 
 339   
 340                  # Define file name for peak list. 
 341                  FNAME = "%s_%s_%s_%s_max_standard.ser"%(I, deltadof2, dpwr2slock, ncyc) 
 342                  sp_id = "%s_%s_%s_%s"%(I, deltadof2, dpwr2slock, ncyc) 
 343   
 344                  # Load the peak intensities. 
 345                  self.interpreter.spectrum.read_intensities(file=FNAME, dir=data_path+sep+'peak_lists', spectrum_id=sp_id, int_method='height') 
 346   
 347                  # Set the peak intensity errors, as defined as the baseplane RMSD. 
 348                  self.interpreter.spectrum.baseplane_rmsd(error=apod_rmsd, spectrum_id=sp_id) 
 349   
 350                  # Set the relaxation dispersion experiment type. 
 351                  self.interpreter.relax_disp.exp_type(spectrum_id=sp_id, exp_type='R1rho') 
 352   
 353                  # Set The spin-lock field strength, nu1, in Hz 
 354                  self.interpreter.relax_disp.spin_lock_field(spectrum_id=sp_id, field=spin_lock_field_strength) 
 355   
 356                  # Calculating the spin-lock offset in ppm, from offsets values provided in Hz. 
 357                  frq_N15_Hz = yOBS * 1E6 
 358                  offset_ppm_N15 = float(deltadof2) / frq_N15_Hz * 1E6 
 359                  omega_rf_ppm = centerPPM_N15 + offset_ppm_N15 
 360   
 361                  # Set The spin-lock offset, omega_rf, in ppm. 
 362                  self.interpreter.relax_disp.spin_lock_offset(spectrum_id=sp_id, offset=omega_rf_ppm) 
 363   
 364                  # Set the relaxation times (in s). 
 365                  self.interpreter.relax_disp.relax_time(spectrum_id=sp_id, time=time_sl) 
 366   
 367                  # Set the spectrometer frequency. 
 368                  self.interpreter.spectrometer.frequency(id=sp_id, frq=set_sfrq, units='MHz') 
 369   
 370                  # Add to counter 
 371                  j += 1 
 372   
 373   
 374          print("Testing the number of settings") 
 375          print("Number of settings iterations is: %s. Number of cdp.exp_type.keys() is: %s"%(i, len(cdp.exp_type.keys() ) ) ) 
 376          self.assertEqual(70, len(expfileslines)) 
 377          self.assertEqual(69, j) 
 378          self.assertEqual(69, len(cdp.exp_type.keys()) ) 
 379   
 380          # Cluster spins 
 381          for curspin in cluster_ids: 
 382              print("Adding spin %s to cluster"%curspin) 
 383              self.interpreter.relax_disp.cluster('model_cluster', curspin) 
 384   
 385          # De-select for analysis those spins who have not been clustered 
 386          for free_spin in cdp.clustering['free spins']: 
 387              print("Deselecting free spin %s"%free_spin) 
 388              self.interpreter.deselect.spin(spin_id=free_spin, change_all=False) 
 389   
 390   
 391          #Paper         reference values 
 392          #              Resi   Resn         R1_rad_s   R1err_rad_s   R2_rad_s   R2err_rad_s   kEX_rad_s      kEXerr_rad_s  phi_rad2_s2     phierr_rad2_s2    phi_ppm2         phierr_ppm2 
 393          # Scaling rad2_s2 to ppm2: scaling_rad2_s2 = frequency_to_ppm(frq=1/(2*pi), B0=cdp.spectrometer_frq_list[0], isotope='15N')**2 = 3.85167990165e-06 
 394          ds.ref = dict() 
 395          ds.ref[':13@N'] = [13,   'L13N-HN',   1.32394,   0.14687,      8.16007,   1.01237,      13193.82986,   2307.09152,   58703.06446,    22413.09854,      0.2261054135,    0.0863280812] 
 396          ds.ref[':15@N'] = [15,   'R15N-HN',   1.34428,   0.14056,      7.83256,   0.67559,      13193.82986,   2307.09152,   28688.33492,    13480.72253,      0.110498283,     0.051923428] 
 397          ds.ref[':16@N'] = [16,   'T16N-HN',   1.71514,   0.13651,      17.44216,  0.98583,      13193.82986,   2307.09152,   57356.77617,    21892.44205,      0.220919942,     0.084322679] 
 398          ds.ref[':25@N'] = [25,   'Q25N-HN',   1.82412,   0.15809,      9.09447,   2.09215,      13193.82986,   2307.09152,   143111.13431,   49535.80302,      0.5512182797,    0.1907960569] 
 399          ds.ref[':26@N'] = [26,   'Q26N-HN',   1.45746,   0.14127,      10.22801,  0.67116,      13193.82986,   2307.09152,   28187.06876,    13359.01615,      0.1085675662,    0.051454654] 
 400          ds.ref[':28@N'] = [28,   'Q28N-HN',   1.48095,   0.14231,      10.33552,  0.691,        13193.82986,   2307.09152,   30088.0686,     13920.25654,      0.1158896091,    0.0536163723] 
 401          ds.ref[':39@N'] = [39,   'L39N-HN',   1.46094,   0.14514,      8.02194,   0.84649,      13193.82986,   2307.09152,   44130.18538,    18104.55064,      0.1699753481,    0.0697329338] 
 402          ds.ref[':40@N'] = [40,   'M40N-HN',   1.21381,   0.14035,      12.19112,  0.81418,      13193.82986,   2307.09152,   41834.90493,    17319.92156,      0.1611346625,    0.0667107938] 
 403          ds.ref[':41@N'] = [41,   'A41N-HN',   1.29296,   0.14286,      9.29941,   0.66246,      13193.82986,   2307.09152,   26694.8921,     13080.66782,      0.1028201794,    0.0503825453] 
 404          ds.ref[':43@N'] = [43,   'F43N-HN',   1.33626,   0.14352,      12.73816,  1.17386,      13193.82986,   2307.09152,   70347.63797,    26648.30524,      0.2709565833,    0.1026407417] 
 405          ds.ref[':44@N'] = [44,   'I44N-HN',   1.28487,   0.1462,       12.70158,  1.52079,      13193.82986,   2307.09152,   95616.20461,    35307.79817,      0.3682830136,    0.1359943366] 
 406          ds.ref[':45@N'] = [45,   'K45N-HN',   1.59227,   0.14591,      9.54457,   0.95596,      13193.82986,   2307.09152,   53849.7826,     21009.89973,      0.2074121253,    0.0809234085] 
 407          ds.ref[':49@N'] = [49,   'A49N-HN',   1.38521,   0.14148,      4.44842,   0.88647,      13193.82986,   2307.09152,   40686.65286,    18501.20774,      0.1567119631,    0.07126073] 
 408          ds.ref[':52@N'] = [52,   'V52N-HN',   1.57531,   0.15042,      6.51945,   1.43418,      13193.82986,   2307.09152,   93499.92172,    33233.23039,      0.3601317693,    0.1280037656] 
 409          ds.ref[':53@N'] = [53,   'A53N-HN',   1.27214,   0.13823,      4.0705,    0.85485,      13193.82986,   2307.09152,   34856.18636,    17505.02393,      0.1342548725,    0.0674237488] 
 410   
 411          ds.guess = dict() 
 412          ds.guess[':13@N'] = [13,   'L13N-HN',   1.32394,   0.14687,      8.16007,   1.01237,      13193.82986,   2307.09152,   58703.06446,    22413.09854,      0.2261054135,    0.0863280812] 
 413          ds.guess[':15@N'] = [15,   'R15N-HN',   1.34428,   0.14056,      7.83256,   0.67559,      13193.82986,   2307.09152,   28688.33492,    13480.72253,      0.110498283,     0.051923428] 
 414          ds.guess[':16@N'] = [16,   'T16N-HN',   1.71514,   0.13651,      17.44216,  0.98583,      13193.82986,   2307.09152,   57356.77617,    21892.44205,      0.220919942,     0.084322679] 
 415          ds.guess[':25@N'] = [25,   'Q25N-HN',   1.82412,   0.15809,      9.09447,   2.09215,      13193.82986,   2307.09152,   143111.13431,   49535.80302,      0.5512182797,    0.1907960569] 
 416          ds.guess[':26@N'] = [26,   'Q26N-HN',   1.45746,   0.14127,      10.22801,  0.67116,      13193.82986,   2307.09152,   28187.06876,    13359.01615,      0.1085675662,    0.051454654] 
 417          ds.guess[':28@N'] = [28,   'Q28N-HN',   1.48095,   0.14231,      10.33552,  0.691,        13193.82986,   2307.09152,   30088.0686,     13920.25654,      0.1158896091,    0.0536163723] 
 418          ds.guess[':39@N'] = [39,   'L39N-HN',   1.46094,   0.14514,      8.02194,   0.84649,      13193.82986,   2307.09152,   44130.18538,    18104.55064,      0.1699753481,    0.0697329338] 
 419          ds.guess[':40@N'] = [40,   'M40N-HN',   1.21381,   0.14035,      12.19112,  0.81418,      13193.82986,   2307.09152,   41834.90493,    17319.92156,      0.1611346625,    0.0667107938] 
 420          ds.guess[':41@N'] = [41,   'A41N-HN',   1.29296,   0.14286,      9.29941,   0.66246,      13193.82986,   2307.09152,   26694.8921,     13080.66782,      0.1028201794,    0.0503825453] 
 421          ds.guess[':43@N'] = [43,   'F43N-HN',   1.33626,   0.14352,      12.73816,  1.17386,      13193.82986,   2307.09152,   70347.63797,    26648.30524,      0.2709565833,    0.1026407417] 
 422          ds.guess[':44@N'] = [44,   'I44N-HN',   1.28487,   0.1462,       12.70158,  1.52079,      13193.82986,   2307.09152,   95616.20461,    35307.79817,      0.3682830136,    0.1359943366] 
 423          ds.guess[':45@N'] = [45,   'K45N-HN',   1.59227,   0.14591,      9.54457,   0.95596,      13193.82986,   2307.09152,   53849.7826,     21009.89973,      0.2074121253,    0.0809234085] 
 424          ds.guess[':49@N'] = [49,   'A49N-HN',   1.38521,   0.14148,      4.44842,   0.88647,      13193.82986,   2307.09152,   40686.65286,    18501.20774,      0.1567119631,    0.07126073] 
 425          ds.guess[':52@N'] = [52,   'V52N-HN',   1.57531,   0.15042,      6.51945,   1.43418,      13193.82986,   2307.09152,   93499.92172,    33233.23039,      0.3601317693,    0.1280037656] 
 426          ds.guess[':53@N'] = [53,   'A53N-HN',   1.27214,   0.13823,      4.0705,    0.85485,      13193.82986,   2307.09152,   34856.18636,    17505.02393,      0.1342548725,    0.0674237488] 
 427   
 428          # Assign guess values. 
 429          for spin, spin_id in spin_loop(return_id=True): 
 430              if spin_id in cluster_ids: 
 431                  print("spin_id %s in cluster ids"%(spin_id)) 
 432                  spin.kex = ds.guess[spin_id][6] 
 433                  spin.phi_ex = ds.guess[spin_id][10] 
 434              else: 
 435                  print("spin_id %s NOT in cluster ids"%(spin_id)) 
 436   
 437          if read_R1: 
 438              # Read the R1 data 
 439              self.interpreter.relax_data.read(ri_id='R1', ri_type='R1', frq=cdp.spectrometer_frq_list[0], file='R1_fitted_values.txt', dir=data_path, mol_name_col=1, res_num_col=2, res_name_col=3, spin_num_col=4, spin_name_col=5, data_col=6, error_col=7) 
 440   
 441   
 442 -    def setup_hansen_cpmg_data(self, model=None): 
 443          """Set up the data for the test_hansen_cpmg_data_*() system tests. 
 444   
 445          @keyword model: The name of the model which will be tested. 
 446          @type model:    str 
 447          """ 
 448   
 449          # Create the data pipe and load the base data. 
 450          data_path = status.install_path + sep+'test_suite'+sep+'shared_data'+sep+'dispersion'+sep+'Hansen' 
 451          self.interpreter.pipe.create(pipe_name='base pipe', pipe_type='relax_disp') 
 452          self.interpreter.results.read(data_path+sep+'base_pipe') 
 453          self.interpreter.deselect.spin(':4') 
 454   
 455          # Set the nuclear isotope data. 
 456          self.interpreter.spin.isotope('15N') 
 457   
 458          # Create the R2eff data pipe and load the results. 
 459          self.interpreter.pipe.create(pipe_name='R2eff - relax_disp', pipe_type='relax_disp') 
 460          self.interpreter.pipe.switch(pipe_name='R2eff - relax_disp') 
 461          self.interpreter.results.read(data_path+sep+'r2eff_pipe') 
 462          self.interpreter.deselect.spin(':4') 
 463   
 464          # The model data pipe. 
 465          pipe_name = "%s - relax_disp" % model 
 466          self.interpreter.pipe.copy(pipe_from='base pipe', pipe_to=pipe_name, bundle_to='relax_disp') 
 467          self.interpreter.pipe.switch(pipe_name=pipe_name) 
 468   
 469          # Set the model. 
 470          self.interpreter.relax_disp.select_model(model=model) 
 471   
 472          # Copy the data. 
 473          self.interpreter.value.copy(pipe_from='R2eff - relax_disp', pipe_to=pipe_name, param='r2eff') 
 474   
 475   
 476 -    def setup_kteilum_fmpoulsen_makke_cpmg_data(self, model=None, expfolder=None): 
 477          """Set up the data for the test_kteilum_fmpoulsen_makke_cpmg_data_*() system tests. 
 478   
 479          @keyword model: The name of the model which will be tested. 
 480          @type model:    str 
 481          """ 
 482   
 483          # Create the data pipe and load the base data. 
 484          data_path = status.install_path + sep+'test_suite'+sep+'shared_data'+sep+'dispersion'+sep+'KTeilum_FMPoulsen_MAkke_2006'+sep+expfolder 
 485          self.interpreter.pipe.create(pipe_name='base pipe', pipe_type='relax_disp') 
 486          self.interpreter.results.read(data_path+sep+'ini_setup_trunc') 
 487   
 488          # Create the R2eff data pipe and load the results. 
 489          self.interpreter.pipe.create(pipe_name='R2eff', pipe_type='relax_disp') 
 490          self.interpreter.pipe.switch(pipe_name='R2eff') 
 491          self.interpreter.results.read(data_path+sep+'r2eff_pipe_trunc') 
 492   
 493          # The model data pipe. 
 494          pipe_name = "%s - relax_disp" % model 
 495          self.interpreter.pipe.copy(pipe_from='base pipe', pipe_to=pipe_name, bundle_to='relax_disp') 
 496          self.interpreter.pipe.switch(pipe_name=pipe_name) 
 497   
 498          # Set the model. 
 499          self.interpreter.relax_disp.select_model(model=model) 
 500   
 501          # Copy the data. 
 502          self.interpreter.value.copy(pipe_from='R2eff', pipe_to=pipe_name, param='r2eff') 
 503   
 504   
 505 -    def setup_korzhnev_2005_data(self, data_list=[]): 
 506          """Set up the data for the test_korzhnev_2005_data_*() system tests using the 'NS MMQ 2-site' model. 
 507   
 508          This loads the proton-heteronuclear SQ, ZQ, DQ, and MQ (MMQ) data from: 
 509   
 510              - Dmitry M. Korzhnev, Philipp Neudecker, Anthony Mittermaier, Vladislav Yu. Orekhov, and Lewis E. Kay (2005)  Multiple-site exchange in proteins studied with a suite of six NMR relaxation dispersion experiments: An application to the folding of a Fyn SH3 domain mutant.  127, 15602-15611 (U{DOI: 10.1021/ja054550e<http://dx.doi.org/10.1021/ja054550e>}). 
 511   
 512          It consists of the 1H SQ, 15N SQ, ZQ, DQ, 1H MQ and 15N MQ data for residue Asp 9 of the Fyn SH3 domain mutant. 
 513   
 514   
 515          @keyword data_list: The list of data to load.  It can contain 'SQ', '1H SQ', 'ZQ', 'DQ', 'MQ', and '1H MQ'. 
 516          @type data_list:    list of str 
 517          """ 
 518   
 519          # Create the data pipe and load the base data. 
 520          data_path = status.install_path + sep+'test_suite'+sep+'shared_data'+sep+'dispersion'+sep+'Korzhnev_et_al_2005' 
 521          self.interpreter.pipe.create(pipe_name='Korzhnev et al., 2005', pipe_type='relax_disp') 
 522   
 523          # Create the spin system. 
 524          self.interpreter.spin.create(res_name='Asp', res_num=9, spin_name='H') 
 525          self.interpreter.spin.create(res_name='Asp', res_num=9, spin_name='N') 
 526          self.interpreter.spin.element('H', spin_id='@H') 
 527          self.interpreter.spin.element('N', spin_id='@N') 
 528          self.interpreter.spin.isotope('1H', spin_id='@H') 
 529          self.interpreter.spin.isotope('15N', spin_id='@N') 
 530   
 531          # Define the magnetic dipole-dipole relaxation interaction. 
 532          self.interpreter.interatom.define(spin_id1=':9@N', spin_id2=':9@H', direct_bond=True) 
 533   
 534          # The spectral data - experiment ID, R2eff file name, experiment type, spin ID string, spectrometer frequency in Hertz, relaxation time. 
 535          data = [ 
 536              ['1H SQ', '1H_SQ_CPMG_500_MHz',  'hs_500.res', EXP_TYPE_CPMG_PROTON_SQ, ':9@H', 500e6, 0.03], 
 537              ['1H SQ', '1H_SQ_CPMG_600_MHz',  'hs_600.res', EXP_TYPE_CPMG_PROTON_SQ, ':9@H', 600e6, 0.03], 
 538              ['1H SQ', '1H_SQ_CPMG_800_MHz',  'hs_800.res', EXP_TYPE_CPMG_PROTON_SQ, ':9@H', 800e6, 0.03], 
 539              ['SQ',    '15N_SQ_CPMG_500_MHz', 'ns_500.res', EXP_TYPE_CPMG_SQ,        ':9@N', 500e6, 0.04], 
 540              ['SQ',    '15N_SQ_CPMG_600_MHz', 'ns_600.res', EXP_TYPE_CPMG_SQ,        ':9@N', 600e6, 0.04], 
 541              ['SQ',    '15N_SQ_CPMG_800_MHz', 'ns_800.res', EXP_TYPE_CPMG_SQ,        ':9@N', 800e6, 0.04], 
 542              ['DQ',    '15N_DQ_CPMG_500_MHz', 'dq_500.res', EXP_TYPE_CPMG_DQ,        ':9@N', 500e6, 0.03], 
 543              ['DQ',    '15N_DQ_CPMG_600_MHz', 'dq_600.res', EXP_TYPE_CPMG_DQ,        ':9@N', 600e6, 0.03], 
 544              ['DQ',    '15N_DQ_CPMG_800_MHz', 'dq_800.res', EXP_TYPE_CPMG_DQ,        ':9@N', 800e6, 0.03], 
 545              ['ZQ',    '15N_ZQ_CPMG_500_MHz', 'zq_500.res', EXP_TYPE_CPMG_ZQ,        ':9@N', 500e6, 0.03], 
 546              ['ZQ',    '15N_ZQ_CPMG_600_MHz', 'zq_600.res', EXP_TYPE_CPMG_ZQ,        ':9@N', 600e6, 0.03], 
 547              ['ZQ',    '15N_ZQ_CPMG_800_MHz', 'zq_800.res', EXP_TYPE_CPMG_ZQ,        ':9@N', 800e6, 0.03], 
 548              ['1H MQ', '1H_MQ_CPMG_500_MHz',  'hm_500.res', EXP_TYPE_CPMG_PROTON_MQ, ':9@H', 500e6, 0.02], 
 549              ['1H MQ', '1H_MQ_CPMG_600_MHz',  'hm_600.res', EXP_TYPE_CPMG_PROTON_MQ, ':9@H', 600e6, 0.02], 
 550              ['1H MQ', '1H_MQ_CPMG_800_MHz',  'hm_800.res', EXP_TYPE_CPMG_PROTON_MQ, ':9@H', 800e6, 0.02], 
 551              ['MQ',    '15N_MQ_CPMG_500_MHz', 'nm_500.res', EXP_TYPE_CPMG_MQ,        ':9@N', 500e6, 0.02], 
 552              ['MQ',    '15N_MQ_CPMG_600_MHz', 'nm_600.res', EXP_TYPE_CPMG_MQ,        ':9@N', 600e6, 0.02], 
 553              ['MQ',    '15N_MQ_CPMG_800_MHz', 'nm_800.res', EXP_TYPE_CPMG_MQ,        ':9@N', 800e6, 0.02] 
 554          ] 
 555          cpmg_frqs_1h_sq = [67.0, 133.0, 267.0, 400.0, 533.0, 667.0, 800.0, 933.0, 1067.0, 1600.0, 2133.0, 2667.0] 
 556          cpmg_frqs_sq = [50.0, 100.0, 150.0, 200.0, 250.0, 300.0, 350.0, 400.0, 450.0, 500.0, 600.0, 700.0, 800.0, 900.0, 1000.0] 
 557          cpmg_frqs_dq = [33.0, 67.0, 133.0, 200.0, 267.0, 333.0, 400.0, 467.0, 533.0, 667.0, 800.0, 933.0, 1067.0] 
 558          cpmg_frqs_zq = [33.0, 67.0, 133.0, 200.0, 267.0, 333.0, 400.0, 467.0, 533.0, 667.0, 800.0, 933.0, 1067.0] 
 559          cpmg_frqs_1h_mq = [50.0, 100.0, 150.0, 200.0, 250.0, 300.0, 400.0, 500.0, 600.0, 700.0, 800.0, 1000.0, 1500.0, 2000.0, 2500.0] 
 560          cpmg_frqs_mq = [50.0, 100.0, 150.0, 200.0, 250.0, 300.0, 350.0, 400.0, 500.0, 600.0, 700.0, 800.0, 900.0, 1000.0] 
 561   
 562          # Loop over the files, reading in the data. 
 563          for data_type, id, file, exp_type, spin_id, H_frq, relax_time in data: 
 564              # Skip undesired data. 
 565              if data_type not in data_list: 
 566                  continue 
 567   
 568              # Alias the CPMG frequencies. 
 569              if data_type == 'SQ': 
 570                  cpmg_frqs = cpmg_frqs_sq 
 571              elif data_type == '1H SQ': 
 572                  cpmg_frqs = cpmg_frqs_1h_sq 
 573              elif data_type == 'DQ': 
 574                  cpmg_frqs = cpmg_frqs_dq 
 575              elif data_type == 'ZQ': 
 576                  cpmg_frqs = cpmg_frqs_zq 
 577              elif data_type == '1H MQ': 
 578                  cpmg_frqs = cpmg_frqs_1h_mq 
 579              elif data_type == 'MQ': 
 580                  cpmg_frqs = cpmg_frqs_mq 
 581   
 582              # Loop over each CPMG frequency. 
 583              for cpmg_frq in cpmg_frqs: 
 584                  # The id. 
 585                  new_id = "%s_%s" % (id, cpmg_frq) 
 586   
 587                  # Set the NMR field strength. 
 588                  self.interpreter.spectrometer.frequency(id=new_id, frq=H_frq) 
 589   
 590                  # Set the relaxation dispersion experiment type. 
 591                  self.interpreter.relax_disp.exp_type(spectrum_id=new_id, exp_type=exp_type) 
 592   
 593                  # Relaxation dispersion CPMG constant time delay T (in s). 
 594                  self.interpreter.relax_disp.relax_time(spectrum_id=new_id, time=relax_time) 
 595   
 596                  # Set the CPMG frequency. 
 597                  self.interpreter.relax_disp.cpmg_setup(spectrum_id=new_id, cpmg_frq=cpmg_frq) 
 598   
 599              # Read the R2eff data. 
 600              self.interpreter.relax_disp.r2eff_read_spin(id=id, file=file, dir=data_path, spin_id=spin_id, disp_point_col=1, data_col=2, error_col=3) 
 601   
 602          # Change the model. 
 603          self.interpreter.relax_disp.select_model('NS MMQ 2-site') 
 604   
 605   
 606 -    def setup_sod1wt_t25(self, pipe_name, pipe_type, pipe_name_r2eff, select_spin_index): 
 607          """Setup of data SOD1-WT CPMG. From paper at U{http://dx.doi.org/10.1073/pnas.0907387106}. 
 608   
 609          Optimisation of Kaare Teilum, Melanie H. Smith, Eike Schulz, Lea C. Christensen, Gleb Solomentseva, Mikael Oliveberg, and Mikael Akkea 2009 
 610          'SOD1-WT' CPMG data to the CR72 dispersion model. 
 611   
 612          This uses the data from paper at U{http://dx.doi.org/10.1073/pnas.0907387106}.  This is CPMG data with a fixed relaxation time period recorded at fields of 500 and 600MHz. 
 613          Data is for experiment at 25 degree Celcius. 
 614          """ 
 615   
 616          # Create the data pipe and load the base data. 
 617          data_path = status.install_path + sep+'test_suite'+sep+'shared_data'+sep+'dispersion'+sep+'sod1wt_t25' 
 618   
 619          # Set experiment settings. sfrq, time_T2, ncyc 
 620          Exps = [ 
 621          ["600MHz", "Z_A", 599.8908617*1E6, 0.06, [28, 0, 4, 32, 60, 2, 10, 16, 8, 20, 50, 18, 40, 6, 12, 0, 24], ["Z_A1", "Z_A15"] ], 
 622          ["500MHz", "Z_B", 499.862139*1E6, 0.04, [20, 0, 16, 10, 36, 2, 12, 4, 22, 18, 40, 14, 26, 8, 32, 24, 6, 28, 0], ["Z_B1", "Z_B18"] ] ] 
 623   
 624          # Create base pipe 
 625          self.interpreter.pipe.create(pipe_name=pipe_name, pipe_type=pipe_type) 
 626   
 627          # Loop throug experiments 
 628          id_lists = [] 
 629          for folder, key, sfrq, time_T2, ncycs, rep_ncyss in Exps: 
 630              # Read spins 
 631              self.interpreter.spectrum.read_spins(file="128_FT.ser", dir=data_path+sep+folder) 
 632              self.interpreter.spectrum.read_spins(file="128_FT.ser", dir=data_path+sep+folder) 
 633   
 634              # Make spectrum id list 
 635              id_list = list(key+str(i) for i in range(len(ncycs))) 
 636              id_lists.append(id_list) 
 637   
 638              # Read intensities 
 639              self.interpreter.spectrum.read_intensities(file="128_FT.ser", dir=data_path+sep+folder, int_method='height', spectrum_id=id_list, int_col=list(range(len(id_list))) ) 
 640   
 641              # Loop over experiments 
 642              for i in range(len(ncycs)): 
 643                  ncyc = ncycs[i] 
 644                  vcpmg = ncyc/time_T2 
 645   
 646                  # Test if spectrum is a reference 
 647                  if float(vcpmg) == 0.0: 
 648                      vcpmg = None 
 649                  else: 
 650                      vcpmg = round(float(vcpmg), 3) 
 651   
 652                  # Set current id 
 653                  current_id = id_list[i] 
 654   
 655                  # Set the current experiment type. 
 656                  self.interpreter.relax_disp.exp_type(spectrum_id=current_id, exp_type='SQ CPMG') 
 657   
 658                  # Set the NMR field strength of the spectrum. 
 659                  self.interpreter.spectrometer.frequency(id=current_id, frq=sfrq, units='Hz') 
 660   
 661                  # Relaxation dispersion CPMG constant time delay T (in s). 
 662                  self.interpreter.relax_disp.relax_time(spectrum_id=current_id, time=time_T2) 
 663   
 664                  # Set the relaxation dispersion CPMG frequencies. 
 665                  self.interpreter.relax_disp.cpmg_setup(spectrum_id=current_id, cpmg_frq=vcpmg) 
 666   
 667          # Define replicated 
 668          self.interpreter.spectrum.replicated(spectrum_ids=Exps[0][5]) 
 669          self.interpreter.spectrum.replicated(spectrum_ids=Exps[1][5]) 
 670   
 671          # Perform error analysis 
 672          self.interpreter.spectrum.error_analysis(subset=id_lists[0]) 
 673          self.interpreter.spectrum.error_analysis(subset=id_lists[1]) 
 674   
 675          # Define isotope 
 676          self.interpreter.spin.isotope(isotope='15N') 
 677   
 678          ############# 
 679   
 680          # Define the 64 residues which was used for Global fitting 
 681          glob_assn = ["G10N-H", "D11N-H", "Q15N-H", "G16N-H", "G37N-H", "G41N-H", "L42N-H", "H43N-H", "H46N-H", "V47N-H", "E49N-H", 
 682          "E50N-H", "E51N-H", "N53N-H", "T54N-H", "G56N-H", "C57N-H", "T58N-H", "G61N-H", "H63aN-H", "F64aN-H", "N65aN-H", 
 683          "L67N-H", "S68N-H", "K70N-H", "G72N-H", "G73N-H", "K75N-H", "E78N-H", "R79N-H", "H80N-H", "V81N-H", "G82N-H", 
 684          "G85N-H", "N86N-H", "V87N-H", "S102N-H", "V103N-H", "I104N-H", "S105N-H", "A111N-H", "I112N-H", "R115N-H", 
 685          "V118N-H", "E121N-H", "A123N-H", "L126N-H", "G127N-H", "K128N-H", "G129N-H", "G130N-H", "N131N-H", "E133N-H", 
 686          "S134N-H", "T135N-H", "T137N-H", "G138N-H", "N139N-H", "A140N-H", "G141N-H", "S142N-H", "R143N-H", "C146N-H", "G147N-H"] 
 687   
 688          # Test number of global 
 689          self.assertEqual(64, len(glob_assn )) 
 690   
 691          ## Turn assignments into relax spin ids. 
 692          # Define regular expression search 
 693          r = re.compile("([a-zA-Z]+)([0-9]+)([a-zA-Z]+)") 
 694   
 695          # Create list to hold regular expression search 
 696          relax_glob_ids = [] 
 697   
 698          # Loop over assignments 
 699          for assn in glob_assn: 
 700              # Make match for the regular search 
 701              m = r.match(assn) 
 702              # Convert to relax spin string 
 703              relax_string = ":%s@%s"%(m.group(2), m.group(3)) 
 704   
 705              # Save the relax spin string and the regular search 
 706              relax_glob_ids.append([m.group(0), m.group(1), m.group(2), m.group(3), relax_string]) 
 707   
 708          ############# Deselect all spins, and select few spins 
 709   
 710          ## Deselect all spins, and select a few for analysis 
 711          self.interpreter.deselect.all() 
 712   
 713          # Select few spins 
 714          for i in select_spin_index: 
 715              self.interpreter.select.spin(spin_id=relax_glob_ids[i][4], change_all=False) 
 716   
 717          ############## 
 718   
 719          # Prepare for R2eff calculation 
 720          self.interpreter.pipe.copy(pipe_from=pipe_name, pipe_to=pipe_name_r2eff) 
 721          self.interpreter.pipe.switch(pipe_name=pipe_name_r2eff) 
 722   
 723          # Select model for points calculation 
 724          MODEL = "R2eff" 
 725          self.interpreter.relax_disp.select_model(model=MODEL) 
 726          # Calculate R2eff values 
 727          self.interpreter.minimise.calculate(verbosity=1) 
 728   
 729   
 730 -    def setup_missing_r1_spins(self): 
 731          """Function for setting up a few spins for the given pipe.""" 
 732   
 733          # Path to file. 
 734          data_path = status.install_path + sep+'test_suite'+sep+'shared_data'+sep+'dispersion'+sep+'Kjaergaard_et_al_2013' 
 735   
 736          # File with spins. 
 737          file = open(data_path+sep+'R1_fitted_values.txt') 
 738          lines = file.readlines() 
 739          file.close() 
 740   
 741          for i, line in enumerate(lines): 
 742              # Make the string test 
 743              line_split = line.split() 
 744   
 745              if line_split[0] == "#": 
 746                  continue 
 747   
 748              mol_name = line_split[0] 
 749              mol_name = None 
 750              res_num = int(line_split[1]) 
 751              res_name = line_split[2] 
 752              spin_num = line_split[3] 
 753              spin_num = None 
 754              spin_name = line_split[4] 
 755   
 756              # Create the spin. 
 757              self.interpreter.spin.create(spin_name=spin_name, spin_num=spin_num, res_name=res_name, res_num=res_num, mol_name=mol_name) 
 758   
 759   
 760 -    def setup_tp02_data_to_ns_r1rho_2site(self, clustering=False): 
 761          """Setup data for the test of relaxation dispersion 'NS R1rho 2-site' model fitting against the 'TP02' test data.""" 
 762   
 763          # Reset. 
 764          self.interpreter.reset() 
 765   
 766          # Create the data pipe and load the base data. 
 767          data_path = status.install_path + sep+'test_suite'+sep+'shared_data'+sep+'dispersion'+sep+'r1rho_off_res_tp02' 
 768          self.interpreter.state.load(data_path+sep+'r2eff_values') 
 769   
 770          # The model data pipe. 
 771          model = 'NS R1rho 2-site' 
 772          pipe_name = "%s - relax_disp" % model 
 773          self.interpreter.pipe.copy(pipe_from='base pipe', pipe_to=pipe_name, bundle_to='relax_disp') 
 774          self.interpreter.pipe.switch(pipe_name=pipe_name) 
 775   
 776          # Set the model. 
 777          self.interpreter.relax_disp.select_model(model=model) 
 778   
 779          # Copy the data. 
 780          self.interpreter.value.copy(pipe_from='R2eff', pipe_to=pipe_name, param='r2eff') 
 781   
 782          # Alias the spins. 
 783          spin1 = cdp.mol[0].res[0].spin[0] 
 784          spin2 = cdp.mol[0].res[1].spin[0] 
 785   
 786          # The R20 keys. 
 787          r20_key1 = generate_r20_key(exp_type=EXP_TYPE_R1RHO, frq=500e6) 
 788          r20_key2 = generate_r20_key(exp_type=EXP_TYPE_R1RHO, frq=800e6) 
 789   
 790          # Set the initial parameter values. 
 791          spin1.r2 = {r20_key1: 9.9963793866185, r20_key2: 15.0056724422684} 
 792          spin1.pA = 0.779782428085762 
 793          spin1.dw = 7.57855284496424 
 794          spin1.kex = 1116.7911285203 
 795          spin2.r2 = {r20_key1: 11.9983346935434, r20_key2: 18.0076097513337} 
 796          spin2.pA = 0.826666229688602 
 797          spin2.dw = 9.5732624231366 
 798          spin2.kex = 1380.46162655657 
 799   
 800          # Test the values when clustering. 
 801          if clustering: 
 802              self.interpreter.relax_disp.cluster(cluster_id='all', spin_id=":1-100") 
 803   
 804          # Low precision optimisation. 
 805          self.interpreter.minimise.execute(min_algor='simplex', line_search=None, hessian_mod=None, hessian_type=None, func_tol=1e-05, grad_tol=None, max_iter=1000, constraints=True, scaling=True, verbosity=1) 
 806   
 807          # Printout. 
 808          print("\n\nOptimised parameters:\n") 
 809          print("%-20s %-20s %-20s" % ("Parameter", "Value (:1)", "Value (:2)")) 
 810          print("%-20s %20.15g %20.15g" % ("R2 (500 MHz)", spin1.r2[r20_key1], spin2.r2[r20_key1])) 
 811          print("%-20s %20.15g %20.15g" % ("R2 (800 MHz)", spin1.r2[r20_key2], spin2.r2[r20_key2])) 
 812          print("%-20s %20.15g %20.15g" % ("pA", spin1.pA, spin2.pA)) 
 813          print("%-20s %20.15g %20.15g" % ("dw", spin1.dw, spin2.dw)) 
 814          print("%-20s %20.15g %20.15g" % ("kex", spin1.kex, spin2.kex)) 
 815          print("%-20s %20.15g %20.15g\n" % ("chi2", spin1.chi2, spin2.chi2)) 
 816   
 817   
 818 -    def test_baldwin_synthetic(self): 
 819          """Test synthetic data of Andrew J. Baldwin B14 model  whereby the simplification R20A = R20B is assumed. 
 820   
 821          Support requst sr #3154 U{https://gna.org/support/index.php?3154}. 
 822   
 823          This uses the synthetic data from paper U{DOI: 10.1016/j.jmr.2014.02.023 <http://dx.doi.org/10.1016/j.jmr.2014.02.023>} with R20A, R20B = 2. rad/s. 
 824          """ 
 825   
 826          # The path to the data files. 
 827          data_path = status.install_path + sep+'test_suite'+sep+'shared_data'+sep+'dispersion'+sep+'Baldwin_2014' 
 828   
 829          # Create pipe 
 830          pipe_name = 'base pipe' 
 831          pipe_type = 'relax_disp' 
 832          pipe_name_r2eff = "%s_R2eff"%(pipe_name) 
 833   
 834          # Create base pipe 
 835          self.interpreter.pipe.create(pipe_name=pipe_name, pipe_type=pipe_type) 
 836   
 837          # Generate the sequence. 
 838          self.interpreter.spin.create(res_name='Ala', res_num=1, spin_name='H') 
 839   
 840          # Define the isotope. 
 841          self.interpreter.spin.isotope('1H', spin_id='@H') 
 842   
 843          # Build the experiment IDs. 
 844          # Number of cpmg cycles (1 cycle = delay/180/delay/delay/180/delay) 
 845          ncycs = [2, 4, 8, 10, 20, 40, 500] 
 846          ids = [] 
 847          for ncyc in ncycs: 
 848              ids.append('CPMG_%s' % ncyc) 
 849   
 850          print("\n\nThe experiment IDs are %s." % ids) 
 851   
 852          # Set up the metadata for the experiments. 
 853          # This value is used in Baldwin.py. It is the 1H Larmor frequency. 
 854          sfrq = 200. * 1E6 
 855   
 856          # Total time of CPMG block. 
 857          Trelax = 0.04 
 858   
 859          # First set the 
 860          for i in range(len(ids)): 
 861              id = ids[i] 
 862              # Set the spectrometer frequency. 
 863              self.interpreter.spectrometer.frequency(id=id, frq=sfrq) 
 864   
 865              # Set the experiment type. 
 866              self.interpreter.relax_disp.exp_type(spectrum_id=id, exp_type='SQ CPMG') 
 867   
 868              # Set the relaxation dispersion CPMG constant time delay T (in s). 
 869              self.interpreter.relax_disp.relax_time(spectrum_id=id, time=Trelax) 
 870   
 871              # Set the relaxation dispersion CPMG frequencies. 
 872              ncyc = ncycs[i] 
 873              nu_cpmg = ncyc / Trelax 
 874              self.interpreter.relax_disp.cpmg_setup(spectrum_id=id, cpmg_frq=nu_cpmg) 
 875   
 876          # Prepare for R2eff reading. 
 877          self.interpreter.pipe.copy(pipe_from=pipe_name, pipe_to=pipe_name_r2eff) 
 878          self.interpreter.pipe.switch(pipe_name=pipe_name_r2eff) 
 879   
 880          # Try reading the R2eff file. 
 881          self.interpreter.relax_disp.r2eff_read_spin(id="CPMG", file="test_r2a_eq_r2b_w_error.out", dir=data_path, spin_id=':1@H', disp_point_col=1, data_col=2, error_col=3) 
 882   
 883          # Check the global data. 
 884          data = [ 
 885              ['cpmg_frqs', {'CPMG_20': 500.0, 'CPMG_10': 250.0, 'CPMG_40': 1000.0, 'CPMG_4': 100.0, 'CPMG_2': 50.0, 'CPMG_500': 12500.0, 'CPMG_8': 200.0}], 
 886              ['cpmg_frqs_list', list(array(ncycs)/Trelax) ], 
 887              ['dispersion_points', len(ncycs)], 
 888              ['exp_type', {'CPMG_20': 'SQ CPMG', 'CPMG_10': 'SQ CPMG', 'CPMG_40': 'SQ CPMG', 'CPMG_4': 'SQ CPMG', 'CPMG_2': 'SQ CPMG', 'CPMG_500': 'SQ CPMG', 'CPMG_8': 'SQ CPMG'}], 
 889              ['exp_type_list', ['SQ CPMG']], 
 890              ['spectrometer_frq', {'CPMG_20': 200000000.0, 'CPMG_10': 200000000.0, 'CPMG_40': 200000000.0, 'CPMG_4': 200000000.0, 'CPMG_2': 200000000.0, 'CPMG_500': 200000000.0, 'CPMG_8': 200000000.0}], 
 891              ['spectrometer_frq_count', 1], 
 892              ['spectrometer_frq_list', [sfrq]], 
 893              ['spectrum_ids', ['CPMG_2', 'CPMG_4', 'CPMG_8', 'CPMG_10', 'CPMG_20', 'CPMG_40', 'CPMG_500']] 
 894          ] 
 895          for name, value in data: 
 896              # Does it exist? 
 897              self.assert_(hasattr(cdp, name)) 
 898   
 899              # Check the object. 
 900              obj = getattr(cdp, name) 
 901              if not isinstance(data, dict): 
 902                  self.assertEqual(obj, value) 
 903   
 904              # Check the global dictionary data. 
 905              else: 
 906                  for id in ids: 
 907                      self.assertEqual(obj[id], value[id]) 
 908   
 909          # Check the spin data. 
 910          n_data = [ 
 911              [ 50.000000, 10.367900, 0.1], 
 912              [ 100.000000, 10.146849, 0.1], 
 913              [ 200.000000, 9.765987, 0.1], 
 914              [ 250.000000, 9.409789, 0.1], 
 915              [ 500.000000, 5.829819, 0.1], 
 916              [ 1000.000000, 3.191928, 0.1], 
 917              [ 12500.000000, 2.008231, 0.1] 
 918          ] 
 919          for disp_point, value, error in n_data: 
 920              id = 'sq_cpmg_200.00000000_0.000_%.3f' % disp_point 
 921              self.assertEqual(cdp.mol[0].res[0].spin[0].r2eff[id], value) 
 922              self.assertEqual(cdp.mol[0].res[0].spin[0].r2eff_err[id], error) 
 923   
 924          # Generate r20 key. 
 925          r20_key = generate_r20_key(exp_type=EXP_TYPE_CPMG_SQ, frq=sfrq) 
 926   
 927          ## Now prepare for MODEL calculation. 
 928          MODEL = "B14" 
 929   
 930          # Change pipe. 
 931          pipe_name_MODEL = "%s_%s"%(pipe_name, MODEL) 
 932          self.interpreter.pipe.copy(pipe_from=pipe_name_r2eff, pipe_to=pipe_name_MODEL) 
 933          self.interpreter.pipe.switch(pipe_name=pipe_name_MODEL) 
 934   
 935          # Then select model. 
 936          self.interpreter.relax_disp.select_model(model=MODEL) 
 937   
 938          # Store grid and minimisations results. 
 939          grid_results = [] 
 940          mini_results = [] 
 941   
 942          # The grid search size (the number of increments per dimension). 
 943          # If None, use the default values. 
 944          #GRID = None 
 945          GRID = 13 
 946          # Perform Grid Search. 
 947          if GRID: 
 948              # Set the R20 parameters in the default grid search using the minimum R2eff value. 
 949              # This speeds it up considerably. 
 950              self.interpreter.relax_disp.r20_from_min_r2eff(force=False) 
 951   
 952              # Then do grid search. 
 953              self.interpreter.minimise.grid_search(lower=None, upper=None, inc=GRID, constraints=True, verbosity=1) 
 954   
 955              # If no Grid search, set the default values. 
 956          else: 
 957              for param in MODEL_PARAMS[MODEL]: 
 958                  self.interpreter.value.set(param=param, index=None) 
 959                  # Do a grid search, which will store the chi2 value. 
 960              self.interpreter.minimise.grid_search(lower=None, upper=None, inc=1, constraints=True, verbosity=1) 
 961   
 962          # Store result. 
 963          for spin, mol_name, resi, resn, spin_id in spin_loop(full_info=True, return_id=True, skip_desel=True): 
 964              grid_results.append([spin.r2[r20_key], spin.dw, spin.pA, spin.kex, spin.chi2, spin_id, resi, resn]) 
 965   
 966          ## Now do minimisation. 
 967          # Standard parameters are: func_tol = 1e-25, grad_tol = None, max_iter = 10000000, 
 968          set_func_tol = 1e-10 
 969          set_max_iter = 1000 
 970          self.interpreter.minimise.execute(min_algor='simplex', func_tol=set_func_tol, max_iter=set_max_iter, constraints=True, scaling=True, verbosity=1) 
 971   
 972          # Store result. 
 973          for spin, mol_name, resi, resn, spin_id in spin_loop(full_info=True, return_id=True, skip_desel=True): 
 974              mini_results.append([spin.r2[r20_key], spin.dw, spin.pA, spin.kex, spin.chi2, spin_id, resi, resn]) 
 975   
 976          # Print results. 
 977          for i in range(len(grid_results)): 
 978              g_r2, g_dw, g_pA, g_kex, g_chi2, g_spin_id, g_resi, g_resn = grid_results[i] 
 979              m_r2, m_dw, m_pA, m_kex, m_chi2, m_spin_id, m_resi, m_resn = mini_results[i] 
 980              print("GRID %s r2=%2.4f dw=%1.4f pA=%1.4f kex=%3.4f chi2=%3.4f spin_id=%s resi=%i resn=%s"%(g_spin_id, g_r2, g_dw, g_pA, g_kex, g_chi2, g_spin_id, g_resi, g_resn)) 
 981              print("MIN  %s r2=%2.4f dw=%1.4f pA=%1.4f kex=%3.4f chi2=%3.4f spin_id=%s resi=%i resn=%s"%(m_spin_id, m_r2, m_dw, m_pA, m_kex, m_chi2, m_spin_id, m_resi, m_resn)) 
 982   
 983          # Reference values from Baldwin.py. 
 984          # Exchange rate = k+ + k- (s-1) 
 985          kex = 1000. 
 986          # Fractional population of excited state k+/kex 
 987          pb = 0.01 
 988          # deltaOmega in ppm 
 989          dw_ppm = 2. 
 990          #relaxation rate of ground (s-1) 
 991          R2g = 2. 
 992          #relaxation rate of excited (s-1) 
 993          R2e = 2. 
 994   
 995          # Test the parameters which created the data. 
 996          # This is for the 1H spin. 
 997          self.assertAlmostEqual(cdp.mol[0].res[0].spin[0].r2[r20_key], R2g, 6) 
 998   
 999          self.assertAlmostEqual(cdp.mol[0].res[0].spin[0].dw, dw_ppm, 6) 
1000          self.assertAlmostEqual(cdp.mol[0].res[0].spin[0].pA, 1-pb, 8) 
1001          self.assertAlmostEqual(cdp.mol[0].res[0].spin[0].kex, kex, 3) 
1002   
1003   
1004 -    def test_baldwin_synthetic_full(self): 
1005          """Test synthetic data of Andrew J. Baldwin B14 model. Support requst sr #3154 U{https://gna.org/support/index.php?3154}. 
1006   
1007          This uses the synthetic data from paper U{DOI: 10.1016/j.jmr.2014.02.023 <http://dx.doi.org/10.1016/j.jmr.2014.02.023>}. 
1008          """ 
1009   
1010          # The path to the data files. 
1011          data_path = status.install_path + sep+'test_suite'+sep+'shared_data'+sep+'dispersion'+sep+'Baldwin_2014' 
1012   
1013          # Create pipe 
1014          pipe_name = 'base pipe' 
1015          pipe_type = 'relax_disp' 
1016          pipe_name_r2eff = "%s_R2eff"%(pipe_name) 
1017   
1018          # Create base pipe 
1019          self.interpreter.pipe.create(pipe_name=pipe_name, pipe_type=pipe_type) 
1020   
1021          # Generate the sequence. 
1022          # Generate both a 1H spin, and 15N spin. 
1023          self.interpreter.spin.create(res_name='Ala', res_num=1, spin_name='H') 
1024   
1025          # Define the isotope. 
1026          self.interpreter.spin.isotope('1H', spin_id='@H') 
1027   
1028          # Build the experiment IDs. 
1029          # Number of cpmg cycles (1 cycle = delay/180/delay/delay/180/delay) 
1030          ncycs = [2, 4, 8, 10, 20, 40, 500] 
1031          ids = [] 
1032          for ncyc in ncycs: 
1033              ids.append('CPMG_%s' % ncyc) 
1034   
1035          print("\n\nThe experiment IDs are %s." % ids) 
1036   
1037          # Set up the metadata for the experiments. 
1038          # This value is used in Baldwin.py. It is the 1H Larmor frequency. 
1039          sfrq = 200. * 1E6 
1040   
1041          # Total time of CPMG block. 
1042          Trelax = 0.04 
1043   
1044          # First set the 
1045          for i in range(len(ids)): 
1046              id = ids[i] 
1047              # Set the spectrometer frequency. 
1048              self.interpreter.spectrometer.frequency(id=id, frq=sfrq) 
1049   
1050              # Set the experiment type. 
1051              self.interpreter.relax_disp.exp_type(spectrum_id=id, exp_type='SQ CPMG') 
1052   
1053              # Set the relaxation dispersion CPMG constant time delay T (in s). 
1054              self.interpreter.relax_disp.relax_time(spectrum_id=id, time=Trelax) 
1055   
1056              # Set the relaxation dispersion CPMG frequencies. 
1057              ncyc = ncycs[i] 
1058              nu_cpmg = ncyc / Trelax 
1059              self.interpreter.relax_disp.cpmg_setup(spectrum_id=id, cpmg_frq=nu_cpmg) 
1060   
1061          # Prepare for R2eff reading. 
1062          self.interpreter.pipe.copy(pipe_from=pipe_name, pipe_to=pipe_name_r2eff) 
1063          self.interpreter.pipe.switch(pipe_name=pipe_name_r2eff) 
1064   
1065          # Try reading the R2eff file. 
1066          self.interpreter.relax_disp.r2eff_read_spin(id="CPMG", file="test_w_error.out", dir=data_path, spin_id=':1@H', disp_point_col=1, data_col=2, error_col=3) 
1067   
1068          # Check the global data. 
1069          data = [ 
1070              ['cpmg_frqs', {'CPMG_20': 500.0, 'CPMG_10': 250.0, 'CPMG_40': 1000.0, 'CPMG_4': 100.0, 'CPMG_2': 50.0, 'CPMG_500': 12500.0, 'CPMG_8': 200.0}], 
1071              ['cpmg_frqs_list', list(array(ncycs)/Trelax) ], 
1072              ['dispersion_points', len(ncycs)], 
1073              ['exp_type', {'CPMG_20': 'SQ CPMG', 'CPMG_10': 'SQ CPMG', 'CPMG_40': 'SQ CPMG', 'CPMG_4': 'SQ CPMG', 'CPMG_2': 'SQ CPMG', 'CPMG_500': 'SQ CPMG', 'CPMG_8': 'SQ CPMG'}], 
1074              ['exp_type_list', ['SQ CPMG']], 
1075              ['spectrometer_frq', {'CPMG_20': 200000000.0, 'CPMG_10': 200000000.0, 'CPMG_40': 200000000.0, 'CPMG_4': 200000000.0, 'CPMG_2': 200000000.0, 'CPMG_500': 200000000.0, 'CPMG_8': 200000000.0}], 
1076              ['spectrometer_frq_count', 1], 
1077              ['spectrometer_frq_list', [sfrq]], 
1078              ['spectrum_ids', ['CPMG_2', 'CPMG_4', 'CPMG_8', 'CPMG_10', 'CPMG_20', 'CPMG_40', 'CPMG_500']] 
1079          ] 
1080          for name, value in data: 
1081              # Does it exist? 
1082              self.assert_(hasattr(cdp, name)) 
1083   
1084              # Check the object. 
1085              obj = getattr(cdp, name) 
1086              if not isinstance(data, dict): 
1087                  self.assertEqual(obj, value) 
1088   
1089              # Check the global dictionary data. 
1090              else: 
1091                  for id in ids: 
1092                      self.assertEqual(obj[id], value[id]) 
1093   
1094          # Check the spin data. 
1095          n_data = [ 
1096              [ 50.000000, 10.286255, 0.1], 
1097              [ 100.000000, 10.073083, 0.1], 
1098              [ 200.000000, 9.692746, 0.1], 
1099              [ 250.000000, 9.382441, 0.1], 
1100              [ 500.000000, 6.312396, 0.1], 
1101              [ 1000.000000, 3.957029, 0.1], 
1102              [ 12500.000000, 2.880420, 0.1] 
1103          ] 
1104          for disp_point, value, error in n_data: 
1105              id = 'sq_cpmg_200.00000000_0.000_%.3f' % disp_point 
1106              self.assertEqual(cdp.mol[0].res[0].spin[0].r2eff[id], value) 
1107              self.assertEqual(cdp.mol[0].res[0].spin[0].r2eff_err[id], error) 
1108   
1109          # Generate r20 key. 
1110          r20_key = generate_r20_key(exp_type=EXP_TYPE_CPMG_SQ, frq=sfrq) 
1111   
1112          ## Now prepare for MODEL calculation. 
1113          MODEL = "B14 full" 
1114   
1115          # Change pipe. 
1116          pipe_name_MODEL = "%s_%s"%(pipe_name, MODEL) 
1117          self.interpreter.pipe.copy(pipe_from=pipe_name_r2eff, pipe_to=pipe_name_MODEL) 
1118          self.interpreter.pipe.switch(pipe_name=pipe_name_MODEL) 
1119   
1120          # Then select model. 
1121          self.interpreter.relax_disp.select_model(model=MODEL) 
1122   
1123          # Store grid and minimisations results. 
1124          grid_results = [] 
1125          mini_results = [] 
1126          clust_results = [] 
1127   
1128          # The grid search size (the number of increments per dimension). 
1129          # If None, use the default values. 
1130          #GRID = None 
1131          GRID = 13 
1132          # Perform Grid Search. 
1133          if GRID: 
1134              # Set the R20 parameters in the default grid search using the minimum R2eff value. 
1135              # This speeds it up considerably. 
1136              self.interpreter.relax_disp.r20_from_min_r2eff(force=False) 
1137   
1138              # Then do grid search. 
1139              self.interpreter.minimise.grid_search(lower=None, upper=None, inc=GRID, constraints=True, verbosity=1) 
1140   
1141              # If no Grid search, set the default values. 
1142          else: 
1143              for param in MODEL_PARAMS[MODEL]: 
1144                  self.interpreter.value.set(param=param, index=None) 
1145                  # Do a grid search, which will store the chi2 value. 
1146              self.interpreter.minimise.grid_search(lower=None, upper=None, inc=1, constraints=True, verbosity=1) 
1147   
1148          # Store result. 
1149          for spin, mol_name, resi, resn, spin_id in spin_loop(full_info=True, return_id=True, skip_desel=True): 
1150              grid_results.append([spin.r2a[r20_key], spin.r2b[r20_key], spin.dw, spin.pA, spin.kex, spin.chi2, spin_id, resi, resn]) 
1151   
1152          ## Now do minimisation. 
1153          # Standard parameters are: func_tol = 1e-25, grad_tol = None, max_iter = 10000000, 
1154          set_func_tol = 1e-11 
1155          set_max_iter = 10000 
1156          self.interpreter.minimise.execute(min_algor='simplex', func_tol=set_func_tol, max_iter=set_max_iter, constraints=True, scaling=True, verbosity=1) 
1157   
1158          # Store result. 
1159          for spin, mol_name, resi, resn, spin_id in spin_loop(full_info=True, return_id=True, skip_desel=True): 
1160              mini_results.append([spin.r2a[r20_key], spin.r2b[r20_key], spin.dw, spin.pA, spin.kex, spin.chi2, spin_id, resi, resn]) 
1161   
1162          print("\n# Now print before and after minimisation-\n") 
1163   
1164          # Print results. 
1165          for i in range(len(grid_results)): 
1166              g_r2a, g_r2b, g_dw, g_pA, g_kex, g_chi2, g_spin_id, g_resi, g_resn = grid_results[i] 
1167              m_r2a, m_r2b, m_dw, m_pA, m_kex, m_chi2, m_spin_id, m_resi, m_resn = mini_results[i] 
1168              print("GRID %s r2a=%2.4f r2b=%2.4f dw=%1.4f pA=%1.4f kex=%3.4f chi2=%3.4f spin_id=%s resi=%i resn=%s"%(g_spin_id, g_r2a, g_r2b, g_dw, g_pA, g_kex, g_chi2, g_spin_id, g_resi, g_resn)) 
1169              print("MIN  %s r2b=%2.4f r2b=%2.4f dw=%1.4f pA=%1.4f kex=%3.4f chi2=%3.4f spin_id=%s resi=%i resn=%s"%(m_spin_id, m_r2a, m_r2b, m_dw, m_pA, m_kex, m_chi2, m_spin_id, m_resi, m_resn)) 
1170   
1171          # Reference values from Baldwin.py. 
1172          # Exchange rate = k+ + k- (s-1) 
1173          kex = 1000. 
1174          # Fractional population of excited state k+/kex 
1175          pb = 0.01 
1176          # deltaOmega in ppm 
1177          dw_ppm = 2. 
1178          #relaxation rate of ground (s-1) 
1179          R2g = 2. 
1180          #relaxation rate of excited (s-1) 
1181          R2e = 100. 
1182   
1183          # Test the parameters which created the data. 
1184          # This is for the 1H spin. 
1185          self.assertAlmostEqual(cdp.mol[0].res[0].spin[0].r2a[r20_key], R2g, 4) 
1186          self.assertAlmostEqual(cdp.mol[0].res[0].spin[0].r2b[r20_key], R2e, 2) 
1187   
1188          self.assertAlmostEqual(cdp.mol[0].res[0].spin[0].dw, dw_ppm, 6) 
1189          self.assertAlmostEqual(cdp.mol[0].res[0].spin[0].pA, 1-pb, 6) 
1190          self.assertAlmostEqual(cdp.mol[0].res[0].spin[0].kex, kex, 2) 
1191   
1192   
1193 -    def test_bug_21081_disp_cluster_fail(self): 
1194          """U{Bug #21081<https://gna.org/bugs/?21081>} catch, the failure of a cluster analysis when spins are deselected.""" 
1195   
1196          # Clear the data store. 
1197          self.interpreter.reset() 
1198   
1199          # Load the state. 
1200          state = status.install_path + sep+'test_suite'+sep+'shared_data'+sep+'saved_states'+sep+'bug_21081_disp_cluster_fail.bz2' 
1201          self.interpreter.state.load(state, force=True) 
1202   
1203          # Model selection - to catch the failure. 
1204          self.interpreter.model_selection(method='AIC', modsel_pipe='final', bundle='relax_disp', pipes=['No Rex', 'CR72']) 
1205   
1206   
1207 -    def test_bug_21460_disp_cluster_fail(self): 
1208          """U{Bug #21460<https://gna.org/bugs/?21460>} catch, the failure due to a spectrometer frequency having no relaxation data.""" 
1209   
1210          # Clear the data store. 
1211          self.interpreter.reset() 
1212   
1213          # Load the state. 
1214          state = status.install_path + sep+'test_suite'+sep+'shared_data'+sep+'saved_states'+sep+'bug_21460_bad_fields.bz2' 
1215          self.interpreter.state.load(state, force=True) 
1216   
1217          # Execute the auto-analysis (fast). 
1218          relax_disp.Relax_disp.opt_func_tol = 1e-5 
1219          relax_disp.Relax_disp.opt_max_iterations = 1000 
1220          relax_disp.Relax_disp(pipe_name="origin - relax_disp (Thu Jan  2 13:46:44 2014)", pipe_bundle="relax_disp (Thu Jan  2 13:46:44 2014)", results_dir=self.tmpdir, models=['R2eff', 'No Rex', 'CR72', 'NS CPMG 2-site expanded'], grid_inc=3, mc_sim_num=5, modsel='AIC', pre_run_dir=None, insignificance=1.0, numeric_only=False, mc_sim_all_models=False, eliminate=True) 
1221   
1222   
1223 -    def test_bug_21344_sparse_time_spinlock_acquired_r1rho_fail_relax_disp(self): 
1224          """U{Bug #21665<https://gna.org/bugs/?21344>} catch, the failure of an analysis of a sparse acquired R1rho dataset with missing combinations of time and spin-lock field strengths using auto_analysis.""" 
1225   
1226          # Clear the data store. 
1227          self.interpreter.reset() 
1228   
1229          # Load the state. 
1230          state = status.install_path + sep+'test_suite'+sep+'shared_data'+sep+'dispersion'+sep+'bug_21344_trunc.bz2' 
1231          self.interpreter.state.load(state, force=True) 
1232   
1233          # Execute the auto-analysis (fast). 
1234          relax_disp.Relax_disp.opt_func_tol = 1e-5 
1235          relax_disp.Relax_disp.opt_max_iterations = 1000 
1236          relax_disp.Relax_disp(pipe_name='base pipe', pipe_bundle='relax_disp', results_dir=self.tmpdir, models=['R2eff'], grid_inc=3, mc_sim_num=5, modsel='AIC', pre_run_dir=None, insignificance=1.0, numeric_only=False, mc_sim_all_models=False, eliminate=True) 
1237   
1238   
1239 -    def test_bug_21665_cpmg_two_fields_two_delaytimes_fail_calc(self): 
1240          """U{Bug #21665<https://gna.org/bugs/?21665>} catch, the failure due to a a CPMG analysis recorded at two fields at two delay times, using minimise.calculate().""" 
1241   
1242          # Clear the data store. 
1243          self.interpreter.reset() 
1244   
1245          # Load the state. 
1246          state = status.install_path + sep+'test_suite'+sep+'shared_data'+sep+'dispersion'+sep+'bug_21665.bz2' 
1247          self.interpreter.state.load(state, force=True) 
1248   
1249          # Run the calculation. 
1250          self.interpreter.minimise.calculate(verbosity=1) 
1251   
1252   
1253 -    def test_bug_21665_cpmg_two_fields_two_delaytimes_fail_relax_disp(self): 
1254          """U{Bug #21665<https://gna.org/bugs/?21665>} catch, the failure due to a a CPMG analysis recorded at two fields at two delay times using auto_analysis.""" 
1255   
1256          # Clear the data store. 
1257          self.interpreter.reset() 
1258   
1259          # Load the state. 
1260          state = status.install_path + sep+'test_suite'+sep+'shared_data'+sep+'dispersion'+sep+'bug_21665.bz2' 
1261          self.interpreter.state.load(state, force=True) 
1262   
1263          # Execute the auto-analysis (fast). 
1264          relax_disp.Relax_disp.opt_func_tol = 1e-5 
1265          relax_disp.Relax_disp.opt_max_iterations = 1000 
1266          relax_disp.Relax_disp(pipe_name="compare_128_FT_R2eff", pipe_bundle="cpmg_disp_sod1d90a", results_dir=self.tmpdir, models=['R2eff'], grid_inc=3, mc_sim_num=5, modsel='AIC', pre_run_dir=None, insignificance=1.0, numeric_only=False, mc_sim_all_models=False, eliminate=True) 
1267   
1268   
1269 -    def test_bug_21715_clustered_indexerror(self): 
1270          """Catch U{bug #21715<https://gna.org/bugs/?21715>}, the failure of a clustered auto-analysis due to an IndexError.""" 
1271   
1272          # Clear the data store. 
1273          self.interpreter.reset() 
1274   
1275          # Load the state. 
1276          state = status.install_path + sep+'test_suite'+sep+'shared_data'+sep+'dispersion'+sep+'bug_21715_clustered_indexerror'+sep+'state.bz2' 
1277          self.interpreter.state.load(state, force=True) 
1278   
1279          # Execute the auto-analysis (fast). 
1280          pre_run_dir = status.install_path + sep+'test_suite'+sep+'shared_data'+sep+'dispersion'+sep+'bug_21715_clustered_indexerror'+sep+'non_clustered' 
1281          relax_disp.Relax_disp.opt_func_tol = 1e-5 
1282          relax_disp.Relax_disp.opt_max_iterations = 1000 
1283          relax_disp.Relax_disp(pipe_name='origin - relax_disp (Sun Feb 23 19:36:51 2014)', pipe_bundle='relax_disp (Sun Feb 23 19:36:51 2014)', results_dir=self.tmpdir, models=['R2eff', 'No Rex'], grid_inc=11, mc_sim_num=2, modsel='AIC', pre_run_dir=pre_run_dir, insignificance=1.0, numeric_only=True, mc_sim_all_models=False, eliminate=True) 
1284   
1285   
1286 -    def test_bug_22146_unpacking_r2a_r2b_cluster_B14(self): 
1287          """Catch U{bug #22146<https://gna.org/bugs/?22146>}, the failure of unpacking R2A and R2B, when performing a clustered B14 full analysis.""" 
1288   
1289          # Base data setup. 
1290          self.setup_bug_22146_unpacking_r2a_r2b_cluster(folder='B14_full', model_analyse = MODEL_B14_FULL) 
1291   
1292   
1293 -    def test_bug_22146_unpacking_r2a_r2b_cluster_CR72(self): 
1294          """Catch U{bug #22146<https://gna.org/bugs/?22146>}, the failure of unpacking R2A and R2B, when performing a clustered CR72 full analysis.""" 
1295   
1296          # Base data setup. 
1297          self.setup_bug_22146_unpacking_r2a_r2b_cluster(folder='CR72_full', model_analyse = MODEL_CR72_FULL) 
1298   
1299   
1300 -    def test_bug_22146_unpacking_r2a_r2b_cluster_NS_3D(self): 
1301          """Catch U{bug #22146<https://gna.org/bugs/?22146>}, the failure of unpacking R2A and R2B, when performing a clustered NS CPMG 2SITE 3D full analysis.""" 
1302   
1303          # Base data setup. 
1304          self.setup_bug_22146_unpacking_r2a_r2b_cluster(folder='ns_cpmg_2site_3d_full', model_analyse = MODEL_NS_CPMG_2SITE_3D_FULL) 
1305   
1306   
1307 -    def test_bug_22146_unpacking_r2a_r2b_cluster_NS_STAR(self): 
1308          """Catch U{bug #22146<https://gna.org/bugs/?22146>}, the failure of unpacking R2A and R2B, when performing a clustered NS CPMG 2SITE STAR full analysis.""" 
1309   
1310          # Base data setup. 
1311          self.setup_bug_22146_unpacking_r2a_r2b_cluster(folder='ns_cpmg_2site_star_full', model_analyse = MODEL_NS_CPMG_2SITE_STAR_FULL, places = 4) 
1312   
1313   
1314 -    def test_bug_22477_grace_write_k_AB_mixed_analysis(self): 
1315          """Catch U{bug #22146<https://gna.org/bugs/?22477>}, the failure of issuing: grace.write(x_data_type='res_num', y_data_type=param) for a mixed CPMG analysis.""" 
1316   
1317          # Clear the data store. 
1318          self.interpreter.reset() 
1319   
1320          # Load the state. 
1321          state = status.install_path + sep+'test_suite'+sep+'shared_data'+sep+'dispersion'+sep+'bug_22477_grace_write_k_AB_mixed_analysis'+sep+'bug_22477_results.bz2' 
1322          self.interpreter.state.load(state, force=True) 
1323   
1324          param = 'k_AB' 
1325   
1326          for spin, spin_id in spin_loop(return_id=True, skip_desel=True): 
1327              print(spin_id, spin.params) 
1328              if param in spin.params: 
1329                  print(spin_id, spin.k_AB, spin.k_AB_err) 
1330   
1331          # Perform write. 
1332          self.interpreter.grace.write(x_data_type='res_num', y_data_type=param, file='%s.agr'%param, dir=self.tmpdir, force=True) 
1333   
1334   
1335          # Test the header of the value.write  parameter r2. 
1336          param = 'r2' 
1337          self.interpreter.value.write(param=param, file='%s.out'%param, dir=self.tmpdir, force=True) 
1338   
1339          file = open(self.tmpdir+sep+'%s.out'%param) 
1340          lines = file.readlines() 
1341          file.close() 
1342   
1343          for i, line in enumerate(lines): 
1344              # Make the string test 
1345              line_split = line.split() 
1346              print(line_split) 
1347   
1348              if len(line_split) > 1: 
1349                  # Break at parameter header. 
1350                  if line_split[0] == "#" and line_split[1] == 'mol_name': 
1351                      nr_split_header = len(line_split) 
1352                      nr_split_header_i = i 
1353                      break 
1354   
1355          # Call the line after. 
1356          line_split_val = lines[nr_split_header_i + 1].split() 
1357          print(line_split_val) 
1358   
1359          # Assert that the number of columns is equal, plus 1 for "#". 
1360          self.assertEqual(nr_split_header, len(line_split_val) + 1) 
1361   
1362          # Test the header of the value.write for parameter r2eff. 
1363          param = 'r2eff' 
1364          self.interpreter.value.write(param=param, file='%s.out'%param, dir=self.tmpdir, force=True) 
1365   
1366          file = open(self.tmpdir+sep+'%s.out'%param) 
1367          lines = file.readlines() 
1368          file.close() 
1369   
1370          for i, line in enumerate(lines): 
1371              # Make the string test 
1372              line_split = line.split() 
1373              print(line_split) 
1374   
1375              if len(line_split) > 1: 
1376                  # Break at parameter header. 
1377                  if line_split[0] == "#" and line_split[1] == 'mol_name': 
1378                      nr_split_header = len(line_split) 
1379                      nr_split_header_i = i 
1380                      break 
1381   
1382          # Call the line after. 
1383          line_split_val = lines[nr_split_header_i + 1].split() 
1384          print(line_split_val) 
1385   
1386          # Assert that the number of columns is equal, plus 1 for "#". 
1387          self.assertEqual(nr_split_header, len(line_split_val) + 1) 
1388   
1389   
1390 -    def test_bug_9999_slow_r1rho_r2eff_error_with_mc(self): 
1391          """Catch U{bug #9999<https://gna.org/bugs/?9999>}, The slow optimisation of R1rho R2eff error estimation with Monte Carlo simulations.""" 
1392   
1393          # Define path to data  
1394          prev_data_path = status.install_path + sep+'test_suite'+sep+'shared_data'+sep+'dispersion'+sep+'Kjaergaard_et_al_2013' +sep+ "check_graphs" +sep+ "mc_2000"  +sep+ "R2eff" 
1395   
1396          # Read data. 
1397          self.interpreter.results.read(prev_data_path + sep + 'results')         
1398   
1399          # Now count number 
1400          graph_nr = 1 
1401          for exp_type, frq, offset, point in loop_exp_frq_offset_point(return_indices=False): 
1402              print("\nGraph nr %i" % graph_nr) 
1403              for time in loop_time(exp_type=exp_type, frq=frq, offset=offset, point=point): 
1404                  print(exp_type, frq, offset, point, time) 
1405              graph_nr += 1 
1406   
1407          ## Possibly do an error analysis. 
1408   
1409          # Check if intensity errors have already been calculated by the user. 
1410          precalc = True 
1411          for spin in spin_loop(skip_desel=True): 
1412              # No structure. 
1413              if not hasattr(spin, 'peak_intensity_err'): 
1414                  precalc = False 
1415                  break 
1416   
1417              # Determine if a spectrum ID is missing from the list. 
1418              for id in cdp.spectrum_ids: 
1419                  if id not in spin.peak_intensity_err: 
1420                      precalc = False 
1421                      break 
1422   
1423          # Skip. 
1424          if precalc: 
1425              print("Skipping the error analysis as it has already been performed.") 
1426   
1427          else: 
1428              # Loop over the spectrometer frequencies. 
1429              for frq in loop_frq(): 
1430                  # Generate a list of spectrum IDs matching the frequency. 
1431                  ids = [] 
1432                  for id in cdp.spectrum_ids: 
1433                      # Check that the spectrometer frequency matches. 
1434                      match_frq = True 
1435                      if frq != None and cdp.spectrometer_frq[id] != frq: 
1436                          match_frq = False 
1437   
1438                      # Add the ID. 
1439                      if match_frq: 
1440                          ids.append(id) 
1441   
1442                  # Run the error analysis on the subset. 
1443                  self.interpreter.spectrum.error_analysis(subset=ids) 
1444   
1445          print("has_exponential_exp_type:", has_exponential_exp_type()) 
1446   
1447          model = 'R2eff' 
1448          self.interpreter.relax_disp.select_model(model) 
1449   
1450          for spin, spin_id in spin_loop(return_id=True, skip_desel=True): 
1451              #delattr(spin, 'r2eff') 
1452              #delattr(spin, 'r2eff_err') 
1453              #delattr(spin, 'i0') 
1454              #delattr(spin, 'i0_err') 
1455              setattr(spin, 'r2eff', {}) 
1456              setattr(spin, 'r2eff_err', {}) 
1457              setattr(spin, 'i0', {}) 
1458              setattr(spin, 'i0_err', {}) 
1459   
1460          # Do Grid Search 
1461          self.interpreter.minimise.grid_search(lower=None, upper=None, inc=21, constraints=True, verbosity=1) 
1462   
1463          # Start dic. 
1464          my_dic = {} 
1465   
1466          # Define counter for maximum elements in the numpy array list 
1467          NE = 0 
1468          NS = 1 
1469          NM = 0 
1470          NO = 0 
1471          ND = 0 
1472          NT = 0 
1473   
1474          for exp_type, frq, offset, point, ei, mi, oi, di in loop_exp_frq_offset_point(return_indices=True): 
1475              # Save to counter. 
1476              if ei > NE: 
1477                  NE = ei 
1478              if mi > NM: 
1479                  NM = mi 
1480              if oi > NO: 
1481                  NO = oi 
1482              if di > ND: 
1483                 ND = di 
1484   
1485              for time, ti in loop_time(exp_type=exp_type, frq=frq, offset=offset, point=point, return_indices=True): 
1486                  # Save to counter. 
1487                  if ti > NT: 
1488                      NT = ti 
1489   
1490          # Add 1 to counter, since index start from 0. 
1491          NE = NE + 1 
1492          NM = NM + 1  
1493          NO = NO + 1 
1494          ND = ND + 1 
1495          NT = NT + 1 
1496   
1497          # Make data array. 
1498          values_arr = zeros([NE, NS, NM, NO, ND, NT]) 
1499          errors_arr = zeros([NE, NS, NM, NO, ND, NT]) 
1500          times_arr = zeros([NE, NS, NM, NO, ND, NT]) 
1501          struct_arr = zeros([NE, NS, NM, NO, ND, NT]) 
1502          param_key_list = [] 
1503   
1504   
1505          # Loop over each spectrometer frequency and dispersion point. 
1506          for cur_spin, mol_name, resi, resn, spin_id in spin_loop(full_info=True, return_id=True, skip_desel=True): 
1507              # Add key to dic. 
1508              my_dic[spin_id] = {} 
1509   
1510              # Generate spin string. 
1511              spin_string = generate_spin_string(spin=cur_spin, mol_name=mol_name, res_num=resi, res_name=resn) 
1512   
1513              # Loop over the parameters. 
1514              #print("Grid optimised parameters for spin: %s" % (spin_string)) 
1515   
1516              for exp_type, frq, offset, point, ei, mi, oi, di in loop_exp_frq_offset_point(return_indices=True): 
1517                  # Generate the param_key. 
1518                  param_key = return_param_key_from_data(exp_type=exp_type, frq=frq, offset=offset, point=point) 
1519   
1520                  # Append key. 
1521                  param_key_list.append(param_key) 
1522   
1523                  # Add key to dic. 
1524                  my_dic[spin_id][param_key] = {} 
1525   
1526                  # Get the value. 
1527                  R2eff_value = getattr(cur_spin, 'r2eff')[param_key] 
1528                  i0_value = getattr(cur_spin, 'i0')[param_key] 
1529   
1530                  # Save to dic. 
1531                  my_dic[spin_id][param_key]['R2eff_value_grid'] = R2eff_value 
1532                  my_dic[spin_id][param_key]['i0_value_grid'] = i0_value 
1533   
1534                  ## Now try do a line of best fit by least squares. 
1535                  # The peak intensities, errors and times. 
1536                  values = [] 
1537                  errors = [] 
1538                  times = [] 
1539                  for time, ti in loop_time(exp_type=exp_type, frq=frq, offset=offset, point=point, return_indices=True): 
1540                      value = average_intensity(spin=cur_spin, exp_type=exp_type, frq=frq, offset=offset, point=point, time=time, sim_index=None) 
1541                      values.append(value) 
1542   
1543                      error = average_intensity(spin=cur_spin, exp_type=exp_type, frq=frq, offset=offset, point=point, time=time, error=True) 
1544                      errors.append(error) 
1545                      times.append(time) 
1546   
1547                      # Save to numpy arrays. 
1548                      values_arr[ei, 0, mi, oi, di, ti] = value 
1549                      errors_arr[ei, 0, mi, oi, di, ti] = error 
1550                      times_arr[ei, 0, mi, oi, di, ti] = time 
1551                      struct_arr[ei, 0, mi, oi, di, ti] = 1.0 
1552   
1553                  # y= A exp(x * k) 
1554                  # w[i] = ln(y[i]) 
1555                  # int[i] = i0 * exp( - times[i] * r2eff); 
1556                  w = log(array(values)) 
1557                  x = - array(times) 
1558                  n = len(times) 
1559   
1560                  b = (sum(x*w) - 1./n * sum(x) * sum(w) ) / ( sum(x**2) - 1./n * (sum(x))**2 ) 
1561                  a = 1./n * sum(w) - b * 1./n * sum(x) 
1562                  R2eff_est = b 
1563                  i0_est = exp(a) 
1564   
1565                  my_dic[spin_id][param_key]['R2eff_est'] = R2eff_est 
1566                  my_dic[spin_id][param_key]['i0_est'] = i0_est 
1567   
1568                  # Print value. 
1569                  #print("%-10s %-6s %-6s %3.1f : %3.1f" % ("Parameter:", 'R2eff', "Value : Estimated:", R2eff_value, R2eff_est)) 
1570                  #print("%-10s %-6s %-6s %3.1f : %3.1f" % ("Parameter:", 'i0', "Value: Estimated:", i0_value, i0_est)) 
1571   
1572   
1573          # Do minimisation. 
1574          set_func_tol = 1e-25 
1575          set_max_iter = int(1e7) 
1576          self.interpreter.minimise.execute(min_algor='simplex', func_tol=set_func_tol, max_iter=set_max_iter, constraints=True, scaling=True, verbosity=1) 
1577   
1578          # Loop over each spectrometer frequency and dispersion point. 
1579          for cur_spin, mol_name, resi, resn, spin_id in spin_loop(full_info=True, return_id=True, skip_desel=True): 
1580              # Generate spin string. 
1581              spin_string = generate_spin_string(spin=cur_spin, mol_name=mol_name, res_num=resi, res_name=resn) 
1582   
1583              # Loop over the parameters. 
1584              print("Optimised parameters for spin: %s" % (spin_string)) 
1585   
1586              for exp_type, frq, offset, point in loop_exp_frq_offset_point(): 
1587                  # Generate the param_key. 
1588                  param_key = return_param_key_from_data(exp_type=exp_type, frq=frq, offset=offset, point=point) 
1589   
1590                  # Get the value. 
1591                  R2eff_value = getattr(cur_spin, 'r2eff')[param_key] 
1592                  i0_value = getattr(cur_spin, 'i0')[param_key] 
1593   
1594                  # Extract from dic. 
1595                  R2eff_value_grid = my_dic[spin_id][param_key]['R2eff_value_grid'] 
1596                  i0_value_grid = my_dic[spin_id][param_key]['i0_value_grid'] 
1597                  R2eff_est = my_dic[spin_id][param_key]['R2eff_est'] 
1598                  i0_est = my_dic[spin_id][param_key]['i0_est'] 
1599   
1600                  # Print value. 
1601                  #print("%-10s %-6s %-6s %3.1f : %3.1f" % ("Parameter:", 'R2eff', "Value : Estimated:", R2eff_value, R2eff_est)) 
1602                  #print("%-10s %-6s %-6s %3.1f : %3.1f" % ("Parameter:", 'i0', "Value: Estimated:", i0_value, i0_est)) 
1603   
1604                  print("%-10s %-6s %-6s %3.1f : %3.1f: %3.1f" % ("Parameter:", 'R2eff', "Grid : Min : Estimated:", R2eff_value_grid, R2eff_value, R2eff_est)) 
1605                  print("%-10s %-6s %-6s %3.1f : %3.1f: %3.1f" % ("Parameter:", 'i0', "Grid : Min : Estimated:", i0_value_grid, i0_value, i0_est)) 
1606   
1607          print(NE, NS, NM, NO, ND, NT) 
1608          for param_key in param_key_list: 
1609              print("        '%s'," % param_key) 
1610          print(values_arr.shape) 
1611   
1612          # Save arrays to profiling. 
1613          data_path = status.install_path + sep+'test_suite'+sep+'shared_data'+sep+'curve_fitting'+sep+'profiling'+sep 
1614          #save(data_path + "values_arr", values_arr) 
1615          #save(data_path + "errors_arr", errors_arr) 
1616          #save(data_path + "times_arr", times_arr) 
1617          #save(data_path + "struct_arr", struct_arr) 
1618   
1619   
1620 -    def test_bug_atul_srivastava(self): 
1621          """Test data from Atul Srivastava.  This is a bug missing raising a Relax Error, since the setup points to a situation where the data 
1622          shows it is exponential fitting, but only one time point is added per file. 
1623   
1624          This follows: U{Thread <http://thread.gmane.org/gmane.science.nmr.relax.user/1718>}: 
1625          This follows: U{Thread <http://thread.gmane.org/gmane.science.nmr.relax.user/1735>}: 
1626          This follows: U{Thread <http://thread.gmane.org/gmane.science.nmr.relax.user/1735/focus=1736>}: 
1627   
1628          """ 
1629   
1630          # Data path. 
1631          data_path = status.install_path + sep+'test_suite'+sep+'shared_data'+sep+'dispersion'+sep+'bug_Atul_Srivastava' 
1632          file = data_path + sep + 'bug_script.py' 
1633   
1634          # Run script. 
1635          self.interpreter.script(file=file, dir=None) 
1636   
1637          # The grid search size (the number of increments per dimension). 
1638          GRID_INC = 11 
1639   
1640          # Check-data. 
1641          ################# 
1642   
1643          # Loop over spins, to see current setup. 
1644          for cur_spin, mol_name, resi, resn, spin_id in spin_loop(full_info=True, return_id=True, skip_desel=True): 
1645              print(mol_name, resi, resn, spin_id) 
1646   
1647          # Loop over setup. 
1648          for id in cdp.exp_type.keys(): 
1649              print(id, cdp.exp_type[id], cdp.spectrometer_frq[id], cdp.spin_lock_offset[id], cdp.spin_lock_nu1[id]) 
1650   
1651   
1652          # Manual minimisation. 
1653          ################# 
1654          if True: 
1655              # Set the model. 
1656              self.interpreter.relax_disp.select_model(MODEL_R2EFF) 
1657   
1658              # Check if intensity errors have already been calculated. 
1659              check_intensity_errors() 
1660   
1661              # Calculate the R2eff values for the fixed relaxation time period data types. 
1662              if cdp.model_type == MODEL_R2EFF and not has_exponential_exp_type(): 
1663                  self.interpreter.minimise.calculate() 
1664   
1665              # Optimise the model. 
1666              else: 
1667                  constraints = False 
1668                  min_algor = 'Newton' 
1669                  with self.assertRaises(RelaxError): 
1670                      self.interpreter.minimise.grid_search(inc=GRID_INC) 
1671   
1672                  with self.assertRaises(RelaxError): 
1673                      self.interpreter.minimise.execute(min_algor=min_algor, constraints=constraints) 
1674          # Inspect. 
1675          if False: 
1676              # Loop over attributes. 
1677              par_attr_list = ['r2eff', 'i0'] 
1678   
1679              # Collect the estimation data. 
1680              my_dic = {} 
1681              param_key_list = [] 
1682              est_keys = [] 
1683              est_key = 'grid' 
1684              est_keys.append(est_key) 
1685              spin_id_list = [] 
1686   
1687              for cur_spin, mol_name, resi, resn, spin_id in spin_loop(full_info=True, return_id=True, skip_desel=True): 
1688                  # Add key to dic. 
1689                  my_dic[spin_id] = {} 
1690   
1691                  # Add key for estimate. 
1692                  my_dic[spin_id][est_key] = {} 
1693   
1694                  # Add spin key to list. 
1695                  spin_id_list.append(spin_id) 
1696   
1697                  # Generate spin string. 
1698                  spin_string = generate_spin_string(spin=cur_spin, mol_name=mol_name, res_num=resi, res_name=resn) 
1699   
1700                  for exp_type, frq, offset, point, ei, mi, oi, di in loop_exp_frq_offset_point(return_indices=True): 
1701                      # Generate the param_key. 
1702                      param_key = return_param_key_from_data(exp_type=exp_type, frq=frq, offset=offset, point=point) 
1703                      #param_key = generate_r20_key(exp_type=exp_type, frq=frq) 
1704   
1705                      # Append key. 
1706                      param_key_list.append(param_key) 
1707   
1708                      # Add key to dic. 
1709                      my_dic[spin_id][est_key][param_key] = {} 
1710   
1711                      # Get the value. 
1712                      # Loop over err attributes. 
1713                      for par_attr in par_attr_list: 
1714                          if hasattr(cur_spin, par_attr): 
1715                              get_par_attr = getattr(cur_spin, par_attr)[param_key] 
1716                          else: 
1717                              get_par_attr = 0.0 
1718   
1719                          # Save to dic. 
1720                          my_dic[spin_id][est_key][param_key][par_attr] = get_par_attr 
1721   
1722                      # Check number of values. 
1723                      values = [] 
1724                      errors = [] 
1725                      times = [] 
1726                      for time, ti in loop_time(exp_type=exp_type, frq=frq, offset=offset, point=point, return_indices=True): 
1727                          value = average_intensity(spin=cur_spin, exp_type=exp_type, frq=frq, offset=offset, point=point, time=time, sim_index=None) 
1728                          values.append(value) 
1729   
1730                          error = average_intensity(spin=cur_spin, exp_type=exp_type, frq=frq, offset=offset, point=point, time=time, error=True) 
1731                          errors.append(error) 
1732                          times.append(time) 
1733   
1734                      # Save to dic. 
1735                      my_dic[spin_id][est_key][param_key]['values'] = values 
1736                      my_dic[spin_id][est_key][param_key]['errors'] = errors 
1737                      my_dic[spin_id][est_key][param_key]['times'] = times 
1738   
1739          # Analysis variables. 
1740          ##################### 
1741   
1742          # The dispersion models. 
1743          MODELS = ['R2eff', 'No Rex'] 
1744   
1745          # The number of Monte Carlo simulations to be used for error analysis at the end of the analysis. 
1746          MC_NUM = 10 
1747   
1748          # A flag which if True will activate Monte Carlo simulations for all models.  Note this will hugely increase the computation time. 
1749          MC_SIM_ALL_MODELS = False 
1750   
1751          # The results directory. 
1752          RESULTS_DIR = ds.tmpdir 
1753   
1754          # The directory of results of an earlier analysis without clustering. 
1755          PRE_RUN_DIR = None 
1756   
1757          # The model selection technique to use. 
1758          MODSEL = 'AIC' 
1759   
1760          # The flag for only using numeric models in the final model selection. 
1761          NUMERIC_ONLY = False 
1762   
1763          # The R1rho value in rad/s by which to judge insignificance.  If the maximum difference between two points on all dispersion curves for a spin is less than this value, that spin will be deselected. 
1764          INSIGNIFICANCE = 1.0 
1765   
1766          # Auto-analysis execution. 
1767          with self.assertRaises(RelaxError): 
1768              relax_disp.Relax_disp(pipe_name='relax_disp', results_dir=RESULTS_DIR, models=MODELS, grid_inc=GRID_INC, mc_sim_num=MC_NUM, modsel=MODSEL, insignificance=INSIGNIFICANCE, numeric_only=NUMERIC_ONLY) 
1769   
1770   
1771 -    def test_bug_negative_intensities_cpmg(self): 
1772          """Test data, where peak intensities are negative in CPMG 
1773   
1774          This uses the data from paper at U{http://dx.doi.org/10.1073/pnas.0509100103}.  This is CPMG data with a fixed relaxation time period.  Experiment in 0.48 M GuHCl (guanidine hydrochloride). 
1775          """ 
1776   
1777          data_path = status.install_path + sep+'test_suite'+sep+'shared_data'+sep+'dispersion'+sep+'KTeilum_FMPoulsen_MAkke_2006'+sep+'bug_neg_int_acbp_cpmg_disp_048MGuHCl_40C_041223' 
1778   
1779          # Create the spins 
1780          self.interpreter.spectrum.read_spins(file="peaks_list_max_standard.ser", dir=data_path) 
1781   
1782          # Name the isotope for field strength scaling. 
1783          self.interpreter.spin.isotope(isotope='15N') 
1784   
1785          # Read the spectrum from NMRSeriesTab file. The "auto" will generate spectrum name of form: Z_A{i} 
1786          self.interpreter.spectrum.read_intensities(file="peaks_list_max_standard.ser", dir=data_path, spectrum_id='auto', int_method='height') 
1787   
1788          # Loop over the spectra settings. 
1789          ncycfile=open(data_path + sep + 'ncyc.txt', 'r') 
1790   
1791          # Make empty ncyclist 
1792          ncyclist = [] 
1793   
1794          i = 0 
1795          for line in ncycfile: 
1796              ncyc = line.split()[0] 
1797              time_T2 = float(line.split()[1]) 
1798              vcpmg = line.split()[2] 
1799              set_sfrq = float(line.split()[3]) 
1800              rmsd_err = float(line.split()[4]) 
1801   
1802              # Test if spectrum is a reference 
1803              if float(vcpmg) == 0.0: 
1804                  vcpmg = None 
1805              else: 
1806                  vcpmg = round(float(vcpmg), 3) 
1807   
1808              # Add ncyc to list 
1809              ncyclist.append(int(ncyc)) 
1810   
1811              # Set the current spectrum id 
1812              current_id = "Z_A%s"%(i) 
1813   
1814              # Set the current experiment type. 
1815              self.interpreter.relax_disp.exp_type(spectrum_id=current_id, exp_type='SQ CPMG') 
1816   
1817              # Set the peak intensity errors, as defined as the baseplane RMSD. 
1818              self.interpreter.spectrum.baseplane_rmsd(error=rmsd_err, spectrum_id=current_id) 
1819   
1820              # Set the NMR field strength of the spectrum. 
1821              self.interpreter.spectrometer.frequency(id=current_id, frq=set_sfrq, units='MHz') 
1822   
1823              # Relaxation dispersion CPMG constant time delay T (in s). 
1824              self.interpreter.relax_disp.relax_time(spectrum_id=current_id, time=time_T2) 
1825   
1826              # Set the relaxation dispersion CPMG frequencies. 
1827              self.interpreter.relax_disp.cpmg_setup(spectrum_id=current_id, cpmg_frq=vcpmg) 
1828   
1829              i += 1 
1830   
1831          # Specify the duplicated spectra. 
1832          self.interpreter.spectrum.replicated(spectrum_ids=['Z_A1', 'Z_A15']) 
1833   
1834          # Delete replicate spectrum 
1835          #self.interpreter.spectrum.delete('Z_A15') 
1836   
1837          MODELS = [MODEL_R2EFF, MODEL_NOREX] 
1838          GRID_INC = 5; MC_NUM = 3; MODSEL = 'AIC' 
1839   
1840          results_dir = ds.tmpdir 
1841   
1842          # Execute 
1843          relax_disp.Relax_disp(pipe_name='relax_disp', results_dir=results_dir, models=MODELS, grid_inc=GRID_INC, mc_sim_num=MC_NUM, modsel=MODSEL) 
1844   
1845          # Check spin less R2eff points. 
1846          for cur_spin, mol_name, resi, resn, spin_id in spin_loop(full_info=True, return_id=True, skip_desel=False): 
1847              # Assert that spin 4, has one less R2eff point, since one of the intensities are negative. 
1848              if spin_id == ':4@N': 
1849                  self.assertEqual(len(cur_spin.r2eff), 14) 
1850              else: 
1851                  self.assertEqual(len(cur_spin.r2eff), 15) 
1852   
1853   
1854 -    def test_check_missing_r1(self): 
1855          """Test of the check_missing_r1() function.""" 
1856   
1857          # Set up some spins. 
1858          self.setup_missing_r1_spins() 
1859   
1860          # Set variables. 
1861          exp_type = 'R1rho' 
1862          frq = 800.1 * 1E6 
1863   
1864          spectrum_id='test' 
1865   
1866          # Set an experiment type to the pipe. 
1867          self.interpreter.relax_disp.exp_type(spectrum_id=spectrum_id, exp_type=exp_type) 
1868   
1869          # Set a frequency to loop through. 
1870          self.interpreter.spectrometer.frequency(id=spectrum_id, frq=frq, units='Hz') 
1871   
1872          # Check R1 for DPL94. 
1873          check_missing_r1_return = check_missing_r1(model=MODEL_DPL94) 
1874          self.assertEqual(check_missing_r1_return, True) 
1875   
1876          # Check R1 for R2eff. 
1877          check_missing_r1_return = check_missing_r1(model=MODEL_R2EFF) 
1878          self.assertEqual(check_missing_r1_return, False) 
1879   
1880          # The path to the data files. 
1881          data_path = status.install_path + sep+'test_suite'+sep+'shared_data'+sep+'dispersion'+sep+'Kjaergaard_et_al_2013' 
1882   
1883          # Now load some R1 data. 
1884          self.interpreter.relax_data.read(ri_id='R1', ri_type='R1', frq=cdp.spectrometer_frq_list[0], file='R1_fitted_values.txt', dir=data_path, mol_name_col=1, res_num_col=2, res_name_col=3, spin_num_col=4, spin_name_col=5, data_col=6, error_col=7) 
1885   
1886          # Check R1. 
1887          check_missing_r1_return = check_missing_r1(model=MODEL_DPL94) 
1888          self.assertEqual(check_missing_r1_return, False) 
1889   
1890   
1891 -    def test_cpmg_synthetic_b14_to_ns3d_cluster(self): 
1892          """Test synthetic cpmg data.  Created with B14, analysed with NS CPMG 2site 3D, for clustered analysis. 
1893   
1894          This is part of: U{Task #7807 <https://gna.org/task/index.php?7807>}: Speed-up of dispersion models for Clustered analysis. 
1895   
1896          This script will produce synthetic CPMG R2eff values according to the selected model, and the fit the selected model. 
1897          """ 
1898   
1899          # Reset. 
1900          #self.interpreter.reset() 
1901   
1902          ## Set Experiments. 
1903          model_create = 'B14' 
1904          #model_create = 'NS CPMG 2-site expanded' 
1905          model_analyse = 'NS CPMG 2-site 3D' 
1906   
1907          # Exp 1 
1908          sfrq_1 = 599.8908617*1E6 
1909          r20_key_1 = generate_r20_key(exp_type=EXP_TYPE_CPMG_SQ, frq=sfrq_1) 
1910          time_T2_1 = 0.06 
1911          ncycs_1 = [2, 4, 8, 10, 20, 30, 40, 60] 
1912          #r2eff_errs_1 = [0.05, -0.05, 0.05, -0.05, 0.05, -0.05, 0.05, -0.05] 
1913          r2eff_errs_1 = [0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0] 
1914          exp_1 = [sfrq_1, time_T2_1, ncycs_1, r2eff_errs_1] 
1915   
1916          sfrq_2 = 499.8908617*1E6 
1917          r20_key_2 = generate_r20_key(exp_type=EXP_TYPE_CPMG_SQ, frq=sfrq_2) 
1918          time_T2_2 = 0.05 
1919          ncycs_2 = [2, 4, 8, 10, 30, 35, 40, 50] 
1920          #r2eff_errs_2 = [0.05, -0.05, 0.05, -0.05, 0.05, -0.05, 0.05, -0.05] 
1921          r2eff_errs_2 = [0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0] 
1922          exp_2 = [sfrq_2, time_T2_2, ncycs_2, r2eff_errs_2] 
1923   
1924          # Collect all exps 
1925          exps = [exp_1, exp_2] 
1926   
1927          spins = [ 
1928              ['Ala', 1, 'N', {'r2': {r20_key_1:10., r20_key_2:11.5}, 'r2a': {r20_key_1:10., r20_key_2:11.5}, 'r2b': {r20_key_1:10., r20_key_2:11.5}, 'kex': 1000., 'pA': 0.95, 'dw': 2.} ], 
1929              ['Ala', 2, 'N', {'r2': {r20_key_1:13., r20_key_2:14.5}, 'r2a': {r20_key_1:13., r20_key_2:14.5}, 'r2b': {r20_key_1:13., r20_key_2:14.5}, 'kex': 1000., 'pA': 0.95, 'dw': 1.} ] 
1930              ] 
1931   
1932          # Collect the data to be used. 
1933          ds.data = [model_create, model_analyse, spins, exps] 
1934   
1935          # The tmp directory. None is the local directory. 
1936          ds.tmpdir = ds.tmpdir 
1937   
1938          # The results directory. None is the local directory. 
1939          #ds.resdir = None 
1940          ds.resdir = ds.tmpdir 
1941   
1942          # Do r20_from_min_r2eff ?. 
1943          ds.r20_from_min_r2eff = True 
1944   
1945          # Remove insignificant level. 
1946          ds.insignificance = 0.0 
1947   
1948          # The grid search size (the number of increments per dimension). 
1949          ds.GRID_INC = None 
1950   
1951          # The do clustering. 
1952          ds.do_cluster = True 
1953   
1954          # The function tolerance.  This is used to terminate minimisation once the function value between iterations is less than the tolerance. 
1955          # The default value is 1e-25. 
1956          ds.set_func_tol = 1e-1 
1957   
1958          # The maximum number of iterations. 
1959          # The default value is 1e7. 
1960          ds.set_max_iter = 1000 
1961   
1962          # The verbosity level. 
1963          ds.verbosity = 1 
1964   
1965          # The rel_change WARNING level. 
1966          ds.rel_change = 0.05 
1967   
1968          # The plot_curves. 
1969          ds.plot_curves = False 
1970   
1971          # The conversion for ShereKhan at http://sherekhan.bionmr.org/. 
1972          ds.sherekhan_input = False 
1973   
1974          # Make a dx map to be opened om OpenDX. To map the hypersurface of chi2, when altering kex, dw and pA. 
1975          ds.opendx = False 
1976   
1977          # The set r2eff err. 
1978          ds.r2eff_err = 0.1 
1979   
1980          # The print result info. 
1981          ds.print_res = True 
1982   
1983          # Execute the script. 
1984          self.interpreter.run(script_file=status.install_path + sep+'test_suite'+sep+'system_tests'+sep+'scripts'+sep+'relax_disp'+sep+'cpmg_synthetic.py') 
1985   
1986          cur_spins = ds.data[2] 
1987          # Compare results. 
1988          for i in range(len(cur_spins)): 
1989              res_name, res_num, spin_name, params = cur_spins[i] 
1990              cur_spin_id = ":%i@%s"%(res_num, spin_name) 
1991              cur_spin = return_spin(cur_spin_id) 
1992   
1993              grid_params = ds.grid_results[i][3] 
1994   
1995              # Extract the clust results. 
1996              min_params = ds.clust_results[i][3] 
1997              # Now read the parameters. 
1998              print("For spin: '%s'"%cur_spin_id) 
1999              for mo_param in cur_spin.params: 
2000                  # The R2 is a dictionary, depending on spectrometer frequency. 
2001                  if isinstance(getattr(cur_spin, mo_param), dict): 
2002                      grid_r2 = grid_params[mo_param] 
2003                      min_r2 = min_params[mo_param] 
2004                      set_r2 = params[mo_param] 
2005                      for key, val in set_r2.items(): 
2006                          grid_r2_frq = grid_r2[key] 
2007                          min_r2_frq = min_r2[key] 
2008                          set_r2_frq = set_r2[key] 
2009                          frq = float(key.split(EXP_TYPE_CPMG_SQ+' - ')[-1].split('MHz')[0]) 
2010                          rel_change = math.sqrt( (min_r2_frq - set_r2_frq)**2/(min_r2_frq)**2 ) 
2011                          print("%s %s %s %s %.1f GRID=%.3f MIN=%.3f SET=%.3f RELC=%.3f"%(cur_spin.model, res_name, cur_spin_id, mo_param, frq, grid_r2_frq, min_r2_frq, set_r2_frq, rel_change) ) 
2012                          if rel_change > ds.rel_change: 
2013                              print("WARNING: rel change level is above %.2f, and is %.4f."%(ds.rel_change, rel_change)) 
2014                              print("###################################") 
2015   
2016                          ## Make test on R2. 
2017                          self.assertAlmostEqual(set_r2_frq, min_r2_frq, 1) 
2018                  else: 
2019                      grid_val = grid_params[mo_param] 
2020                      min_val = min_params[mo_param] 
2021                      set_val = params[mo_param] 
2022                      rel_change = math.sqrt( (min_val - set_val)**2/(min_val)**2 ) 
2023                      print("%s %s %s %s GRID=%.3f MIN=%.3f SET=%.3f RELC=%.3f"%(cur_spin.model, res_name, cur_spin_id, mo_param, grid_val, min_val, set_val, rel_change) ) 
2024                      if rel_change > ds.rel_change: 
2025                          print("WARNING: rel change level is above %.2f, and is %.4f."%(ds.rel_change, rel_change)) 
2026                          print("###################################") 
2027   
2028                      ## Make test on parameters. 
2029                      if mo_param == 'dw': 
2030                          self.assertAlmostEqual(set_val/10, min_val/10, 1) 
2031                      elif mo_param == 'kex': 
2032                          self.assertAlmostEqual(set_val/1000, min_val/1000, 1) 
2033                      elif mo_param == 'pA': 
2034                          self.assertAlmostEqual(set_val, min_val, 2) 
2035   
2036   
2037 -    def test_cpmg_synthetic_b14_to_ns_star_cluster(self): 
2038          """Test synthetic cpmg data.  Created with B14, analysed with NS CPMG 2site STAR, for clustered analysis. 
2039   
2040          This is part of: U{Task #7807 <https://gna.org/task/index.php?7807>}: Speed-up of dispersion models for Clustered analysis. 
2041   
2042          This script will produce synthetic CPMG R2eff values according to the selected model, and the fit the selected model. 
2043          """ 
2044   
2045          # Reset. 
2046          #self.interpreter.reset() 
2047   
2048          ## Set Experiments. 
2049          model_create = 'B14' 
2050          #model_create = 'NS CPMG 2-site expanded' 
2051          model_analyse = 'NS CPMG 2-site star' 
2052   
2053          # Exp 1 
2054          sfrq_1 = 599.8908617*1E6 
2055          r20_key_1 = generate_r20_key(exp_type=EXP_TYPE_CPMG_SQ, frq=sfrq_1) 
2056          time_T2_1 = 0.06 
2057          ncycs_1 = [2, 4, 8, 10, 20, 30, 40, 60] 
2058          #r2eff_errs_1 = [0.05, -0.05, 0.05, -0.05, 0.05, -0.05, 0.05, -0.05] 
2059          r2eff_errs_1 = [0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0] 
2060          exp_1 = [sfrq_1, time_T2_1, ncycs_1, r2eff_errs_1] 
2061   
2062          sfrq_2 = 499.8908617*1E6 
2063          r20_key_2 = generate_r20_key(exp_type=EXP_TYPE_CPMG_SQ, frq=sfrq_2) 
2064          time_T2_2 = 0.05 
2065          ncycs_2 = [2, 4, 8, 10, 30, 35, 40, 50] 
2066          #r2eff_errs_2 = [0.05, -0.05, 0.05, -0.05, 0.05, -0.05, 0.05, -0.05] 
2067          r2eff_errs_2 = [0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0] 
2068          exp_2 = [sfrq_2, time_T2_2, ncycs_2, r2eff_errs_2] 
2069   
2070          # Collect all exps 
2071          exps = [exp_1, exp_2] 
2072   
2073          spins = [ 
2074              ['Ala', 1, 'N', {'r2': {r20_key_1:10., r20_key_2:11.5}, 'r2a': {r20_key_1:10., r20_key_2:11.5}, 'r2b': {r20_key_1:10., r20_key_2:11.5}, 'kex': 1000., 'pA': 0.95, 'dw': 2.} ], 
2075              ['Ala', 2, 'N', {'r2': {r20_key_1:13., r20_key_2:14.5}, 'r2a': {r20_key_1:13., r20_key_2:14.5}, 'r2b': {r20_key_1:13., r20_key_2:14.5}, 'kex': 1000., 'pA': 0.95, 'dw': 1.} ] 
2076              ] 
2077   
2078          # Collect the data to be used. 
2079          ds.data = [model_create, model_analyse, spins, exps] 
2080   
2081          # The tmp directory. None is the local directory. 
2082          ds.tmpdir = ds.tmpdir 
2083   
2084          # The results directory. None is the local directory. 
2085          #ds.resdir = None 
2086          ds.resdir = ds.tmpdir 
2087   
2088          # Do r20_from_min_r2eff ?. 
2089          ds.r20_from_min_r2eff = True 
2090   
2091          # Remove insignificant level. 
2092          ds.insignificance = 0.0 
2093   
2094          # The grid search size (the number of increments per dimension). 
2095          ds.GRID_INC = None 
2096   
2097          # The do clustering. 
2098          ds.do_cluster = True 
2099   
2100          # The function tolerance.  This is used to terminate minimisation once the function value between iterations is less than the tolerance. 
2101          # The default value is 1e-25. 
2102          ds.set_func_tol = 1e-1 
2103   
2104          # The maximum number of iterations. 
2105          # The default value is 1e7. 
2106          ds.set_max_iter = 1000 
2107   
2108          # The verbosity level. 
2109          ds.verbosity = 1 
2110   
2111          # The rel_change WARNING level. 
2112          ds.rel_change = 0.05 
2113   
2114          # The plot_curves. 
2115          ds.plot_curves = False 
2116   
2117          # The conversion for ShereKhan at http://sherekhan.bionmr.org/. 
2118          ds.sherekhan_input = False 
2119   
2120          # Make a dx map to be opened om OpenDX. To map the hypersurface of chi2, when altering kex, dw and pA. 
2121          ds.opendx = False 
2122   
2123          # The set r2eff err. 
2124          ds.r2eff_err = 0.1 
2125   
2126          # The print result info. 
2127          ds.print_res = True 
2128   
2129          # Execute the script. 
2130          self.interpreter.run(script_file=status.install_path + sep+'test_suite'+sep+'system_tests'+sep+'scripts'+sep+'relax_disp'+sep+'cpmg_synthetic.py') 
2131   
2132          cur_spins = ds.data[2] 
2133          # Compare results. 
2134          for i in range(len(cur_spins)): 
2135              res_name, res_num, spin_name, params = cur_spins[i] 
2136              cur_spin_id = ":%i@%s"%(res_num, spin_name) 
2137              cur_spin = return_spin(cur_spin_id) 
2138   
2139              grid_params = ds.grid_results[i][3] 
2140   
2141              # Extract the clust results. 
2142              min_params = ds.clust_results[i][3] 
2143              # Now read the parameters. 
2144              print("For spin: '%s'"%cur_spin_id) 
2145              for mo_param in cur_spin.params: 
2146                  # The R2 is a dictionary, depending on spectrometer frequency. 
2147                  if isinstance(getattr(cur_spin, mo_param), dict): 
2148                      grid_r2 = grid_params[mo_param] 
2149                      min_r2 = min_params[mo_param] 
2150                      set_r2 = params[mo_param] 
2151                      for key, val in set_r2.items(): 
2152                          grid_r2_frq = grid_r2[key] 
2153                          min_r2_frq = min_r2[key] 
2154                          set_r2_frq = set_r2[key] 
2155                          frq = float(key.split(EXP_TYPE_CPMG_SQ+' - ')[-1].split('MHz')[0]) 
2156                          rel_change = math.sqrt( (min_r2_frq - set_r2_frq)**2/(min_r2_frq)**2 ) 
2157                          print("%s %s %s %s %.1f GRID=%.3f MIN=%.3f SET=%.3f RELC=%.3f"%(cur_spin.model, res_name, cur_spin_id, mo_param, frq, grid_r2_frq, min_r2_frq, set_r2_frq, rel_change) ) 
2158                          if rel_change > ds.rel_change: 
2159                              print("WARNING: rel change level is above %.2f, and is %.4f."%(ds.rel_change, rel_change)) 
2160                              print("###################################") 
2161   
2162                          ## Make test on R2. 
2163                          self.assertAlmostEqual(set_r2_frq, min_r2_frq, 1) 
2164                  else: 
2165                      grid_val = grid_params[mo_param] 
2166                      min_val = min_params[mo_param] 
2167                      set_val = params[mo_param] 
2168                      rel_change = math.sqrt( (min_val - set_val)**2/(min_val)**2 ) 
2169                      print("%s %s %s %s GRID=%.3f MIN=%.3f SET=%.3f RELC=%.3f"%(cur_spin.model, res_name, cur_spin_id, mo_param, grid_val, min_val, set_val, rel_change) ) 
2170                      if rel_change > ds.rel_change: 
2171                          print("WARNING: rel change level is above %.2f, and is %.4f."%(ds.rel_change, rel_change)) 
2172                          print("###################################") 
2173   
2174                      ## Make test on parameters. 
2175                      if mo_param == 'dw': 
2176                          self.assertAlmostEqual(set_val/10, min_val/10, 1) 
2177                      elif mo_param == 'kex': 
2178                          self.assertAlmostEqual(set_val/1000, min_val/1000, 1) 
2179                      elif mo_param == 'pA': 
2180                          self.assertAlmostEqual(set_val, min_val, 2) 
2181   
2182   
2183 -    def test_cpmg_synthetic_ns3d_to_cr72(self): 
2184          """Test synthetic cpmg data. 
2185   
2186          This script will produce synthetic CPMG R2eff values according to the NS CPMG 2-site 3D model, and the fit the data with CR72. 
2187          """ 
2188   
2189          # Reset. 
2190          #self.interpreter.reset() 
2191   
2192          ## Set Experiments. 
2193          model_create = 'NS CPMG 2-site 3D' 
2194          #model_create = 'NS CPMG 2-site expanded' 
2195          model_analyse = 'CR72' 
2196          # Exp 1 
2197          sfrq_1 = 599.8908617*1E6 
2198          r20_key_1 = generate_r20_key(exp_type=EXP_TYPE_CPMG_SQ, frq=sfrq_1) 
2199          time_T2_1 = 0.06 
2200          ncycs_1 = [2, 4, 8, 10, 20, 30, 40, 60] 
2201          r2eff_err_1 = [0, 0, 0, 0, 0, 0, 0, 0] 
2202          exp_1 = [sfrq_1, time_T2_1, ncycs_1, r2eff_err_1] 
2203   
2204          sfrq_2 = 499.8908617*1E6 
2205          r20_key_2 = generate_r20_key(exp_type=EXP_TYPE_CPMG_SQ, frq=sfrq_2) 
2206          time_T2_2 = 0.05 
2207          ncycs_2 = [2, 4, 8, 10, 30, 35, 40, 50] 
2208          r2eff_err_2 = [0, 0, 0, 0, 0, 0, 0, 0] 
2209          exp_2 = [sfrq_2, time_T2_2, ncycs_2, r2eff_err_2] 
2210   
2211          # Collect all exps 
2212          exps = [exp_1, exp_2] 
2213   
2214          spins = [ 
2215              ['Ala', 1, 'N', {'r2': {r20_key_1:10., r20_key_2:10.}, 'r2a': {r20_key_1:10., r20_key_2:10.}, 'r2b': {r20_key_1:10., r20_key_2:10.}, 'kex': 1000., 'pA': 0.99, 'dw': 2.} ] 
2216              ] 
2217   
2218          # Collect the data to be used. 
2219          ds.data = [model_create, model_analyse, spins, exps] 
2220   
2221          # The tmp directory. None is the local directory. 
2222          ds.tmpdir = ds.tmpdir 
2223   
2224          # The results directory. None is the local directory. 
2225          #ds.resdir = None 
2226          ds.resdir = ds.tmpdir 
2227   
2228          # Do r20_from_min_r2eff ?. 
2229          ds.r20_from_min_r2eff = True 
2230   
2231          # Remove insignificant level. 
2232          ds.insignificance = 0.0 
2233   
2234          # The grid search size (the number of increments per dimension). 
2235          ds.GRID_INC = 8 
2236   
2237          # The do clustering. 
2238          ds.do_cluster = False 
2239   
2240          # The function tolerance.  This is used to terminate minimisation once the function value between iterations is less than the tolerance. 
2241          # The default value is 1e-25. 
2242          ds.set_func_tol = 1e-9 
2243   
2244          # The maximum number of iterations. 
2245          # The default value is 1e7. 
2246          ds.set_max_iter = 1000 
2247   
2248          # The verbosity level. 
2249          ds.verbosity = 1 
2250   
2251          # The rel_change WARNING level. 
2252          ds.rel_change = 0.05 
2253   
2254          # The plot_curves. 
2255          ds.plot_curves = False 
2256   
2257          # The conversion for ShereKhan at http://sherekhan.bionmr.org/. 
2258          ds.sherekhan_input = False 
2259   
2260          # Make a dx map to be opened om OpenDX. To map the hypersurface of chi2, when altering kex, dw and pA. 
2261          ds.opendx = False 
2262   
2263          # The set r2eff err. 
2264          ds.r2eff_err = 0.1 
2265   
2266          # The print result info. 
2267          ds.print_res = False 
2268   
2269          # Execute the script. 
2270          self.interpreter.run(script_file=status.install_path + sep+'test_suite'+sep+'system_tests'+sep+'scripts'+sep+'relax_disp'+sep+'cpmg_synthetic.py') 
2271   
2272          cur_spins = ds.data[2] 
2273          # Compare results. 
2274          for i in range(len(cur_spins)): 
2275              res_name, res_num, spin_name, params = cur_spins[i] 
2276              cur_spin_id = ":%i@%s"%(res_num, spin_name) 
2277              cur_spin = return_spin(cur_spin_id) 
2278   
2279              grid_params = ds.grid_results[i][3] 
2280              min_params = ds.min_results[i][3] 
2281              # Now read the parameters. 
2282              print("For spin: '%s'"%cur_spin_id) 
2283              for mo_param in cur_spin.params: 
2284                  # The R2 is a dictionary, depending on spectrometer frequency. 
2285                  if isinstance(getattr(cur_spin, mo_param), dict): 
2286                      grid_r2 = grid_params[mo_param] 
2287                      min_r2 = min_params[mo_param] 
2288                      set_r2 = params[mo_param] 
2289                      for key, val in set_r2.items(): 
2290                          grid_r2_frq = grid_r2[key] 
2291                          min_r2_frq = min_r2[key] 
2292                          set_r2_frq = set_r2[key] 
2293                          frq = float(key.split(EXP_TYPE_CPMG_SQ+' - ')[-1].split('MHz')[0]) 
2294                          rel_change = math.sqrt( (min_r2_frq - set_r2_frq)**2/(min_r2_frq)**2 ) 
2295                          print("%s %s %s %s %.1f GRID=%.3f MIN=%.3f SET=%.3f RELC=%.3f"%(cur_spin.model, res_name, cur_spin_id, mo_param, frq, grid_r2_frq, min_r2_frq, set_r2_frq, rel_change) ) 
2296                          if rel_change > ds.rel_change: 
2297                              print("WARNING: rel change level is above %.2f, and is %.4f."%(ds.rel_change, rel_change)) 
2298                              print("###################################") 
2299   
2300                          ## Make test on R2. 
2301                          self.assertAlmostEqual(set_r2_frq, min_r2_frq, 2) 
2302                  else: 
2303                      grid_val = grid_params[mo_param] 
2304                      min_val = min_params[mo_param] 
2305                      set_val = params[mo_param] 
2306                      rel_change = math.sqrt( (min_val - set_val)**2/(min_val)**2 ) 
2307                      print("%s %s %s %s GRID=%.3f MIN=%.3f SET=%.3f RELC=%.3f"%(cur_spin.model, res_name, cur_spin_id, mo_param, grid_val, min_val, set_val, rel_change) ) 
2308                      if rel_change > ds.rel_change: 
2309                          print("WARNING: rel change level is above %.2f, and is %.4f."%(ds.rel_change, rel_change)) 
2310                          print("###################################") 
2311   
2312                      ## Make test on parameters. 
2313                      if mo_param == 'dw': 
2314                          self.assertAlmostEqual(set_val/10, min_val/10, 1) 
2315                      elif mo_param == 'kex': 
2316                          self.assertAlmostEqual(set_val/1000, min_val/1000, 1) 
2317                      elif mo_param == 'pA': 
2318                          self.assertAlmostEqual(set_val, min_val, 3) 
2319   
2320   
2321 -    def test_cpmg_synthetic_ns3d_to_b14(self): 
2322          """Test synthetic cpmg data. 
2323   
2324          This script will produce synthetic CPMG R2eff values according to the NS CPMG 2-site 3D model, and the fit the data with B14. 
2325          Try to catch bug #22021 U{https://gna.org/bugs/index.php?22021}: Model B14 shows bad fitting to data. 
2326          """ 
2327   
2328          # Reset. 
2329          #self.interpreter.reset() 
2330   
2331          ## Set Experiments. 
2332          model_create = 'NS CPMG 2-site 3D' 
2333          #model_create = 'NS CPMG 2-site expanded' 
2334          model_analyse = 'B14' 
2335          # Exp 1 
2336          sfrq_1 = 599.8908617*1E6 
2337          r20_key_1 = generate_r20_key(exp_type=EXP_TYPE_CPMG_SQ, frq=sfrq_1) 
2338          time_T2_1 = 0.06 
2339          ncycs_1 = [2, 4, 8, 10, 20, 30, 40, 60] 
2340          r2eff_err_1 = [0, 0, 0, 0, 0, 0, 0, 0] 
2341          exp_1 = [sfrq_1, time_T2_1, ncycs_1, r2eff_err_1] 
2342   
2343          sfrq_2 = 499.8908617*1E6 
2344          r20_key_2 = generate_r20_key(exp_type=EXP_TYPE_CPMG_SQ, frq=sfrq_2) 
2345          time_T2_2 = 0.05 
2346          ncycs_2 = [2, 4, 8, 10, 30, 35, 40, 50] 
2347          r2eff_err_2 = [0, 0, 0, 0, 0, 0, 0, 0] 
2348          exp_2 = [sfrq_2, time_T2_2, ncycs_2, r2eff_err_2] 
2349   
2350          # Collect all exps 
2351          exps = [exp_1, exp_2] 
2352   
2353          spins = [ 
2354              ['Ala', 1, 'N', {'r2': {r20_key_1:10., r20_key_2:10.}, 'r2a': {r20_key_1:10., r20_key_2:10.}, 'r2b': {r20_key_1:10., r20_key_2:10.}, 'kex': 1000., 'pA': 0.99, 'dw': 2.} ] 
2355              ] 
2356   
2357          # Collect the data to be used. 
2358          ds.data = [model_create, model_analyse, spins, exps] 
2359   
2360          # The tmp directory. None is the local directory. 
2361          ds.tmpdir = ds.tmpdir 
2362   
2363          # The results directory. None is the local directory. 
2364          #ds.resdir = None 
2365          ds.resdir = ds.tmpdir 
2366   
2367          # Do r20_from_min_r2eff ?. 
2368          ds.r20_from_min_r2eff = True 
2369   
2370          # Remove insignificant level. 
2371          ds.insignificance = 0.0 
2372   
2373          # The grid search size (the number of increments per dimension). 
2374          ds.GRID_INC = 8 
2375   
2376          # The do clustering. 
2377          ds.do_cluster = False 
2378   
2379          # The function tolerance.  This is used to terminate minimisation once the function value between iterations is less than the tolerance. 
2380          # The default value is 1e-25. 
2381          ds.set_func_tol = 1e-9 
2382   
2383          # The maximum number of iterations. 
2384          # The default value is 1e7. 
2385          ds.set_max_iter = 1000 
2386   
2387          # The verbosity level. 
2388          ds.verbosity = 1 
2389   
2390          # The rel_change WARNING level. 
2391          ds.rel_change = 0.05 
2392   
2393          # The plot_curves. 
2394          ds.plot_curves = False 
2395   
2396          # The conversion for ShereKhan at http://sherekhan.bionmr.org/. 
2397          ds.sherekhan_input = False 
2398   
2399          # Make a dx map to be opened om OpenDX. To map the hypersurface of chi2, when altering kex, dw and pA. 
2400          ds.opendx = False 
2401   
2402          # The set r2eff err. 
2403          ds.r2eff_err = 0.1 
2404   
2405          # The print result info. 
2406          ds.print_res = False 
2407   
2408          # Execute the script. 
2409          self.interpreter.run(script_file=status.install_path + sep+'test_suite'+sep+'system_tests'+sep+'scripts'+sep+'relax_disp'+sep+'cpmg_synthetic.py') 
2410   
2411          cur_spins = ds.data[2] 
2412          # Compare results. 
2413          for i in range(len(cur_spins)): 
2414              res_name, res_num, spin_name, params = cur_spins[i] 
2415              cur_spin_id = ":%i@%s"%(res_num, spin_name) 
2416              cur_spin = return_spin(cur_spin_id) 
2417   
2418              grid_params = ds.grid_results[i][3] 
2419              min_params = ds.min_results[i][3] 
2420              # Now read the parameters. 
2421              print("For spin: '%s'"%cur_spin_id) 
2422              for mo_param in cur_spin.params: 
2423                  # The R2 is a dictionary, depending on spectrometer frequency. 
2424                  if isinstance(getattr(cur_spin, mo_param), dict): 
2425                      grid_r2 = grid_params[mo_param] 
2426                      min_r2 = min_params[mo_param] 
2427                      set_r2 = params[mo_param] 
2428                      for key, val in set_r2.items(): 
2429                          grid_r2_frq = grid_r2[key] 
2430                          min_r2_frq = min_r2[key] 
2431                          set_r2_frq = set_r2[key] 
2432                          frq = float(key.split(EXP_TYPE_CPMG_SQ+' - ')[-1].split('MHz')[0]) 
2433                          rel_change = math.sqrt( (min_r2_frq - set_r2_frq)**2/(min_r2_frq)**2 ) 
2434                          print("%s %s %s %s %.1f GRID=%.3f MIN=%.3f SET=%.3f RELC=%.3f"%(cur_spin.model, res_name, cur_spin_id, mo_param, frq, grid_r2_frq, min_r2_frq, set_r2_frq, rel_change) ) 
2435                          if rel_change > ds.rel_change: 
2436                              print("WARNING: rel change level is above %.2f, and is %.4f."%(ds.rel_change, rel_change)) 
2437                              print("###################################") 
2438   
2439                          ## Make test on R2. 
2440                          self.assertAlmostEqual(set_r2_frq, min_r2_frq, 2) 
2441                  else: 
2442                      grid_val = grid_params[mo_param] 
2443                      min_val = min_params[mo_param] 
2444                      set_val = params[mo_param] 
2445                      rel_change = math.sqrt( (min_val - set_val)**2/(min_val)**2 ) 
2446                      print("%s %s %s %s GRID=%.3f MIN=%.3f SET=%.3f RELC=%.3f"%(cur_spin.model, res_name, cur_spin_id, mo_param, grid_val, min_val, set_val, rel_change) ) 
2447                      if rel_change > ds.rel_change: 
2448                          print("WARNING: rel change level is above %.2f, and is %.4f."%(ds.rel_change, rel_change)) 
2449                          print("###################################") 
2450   
2451                      ## Make test on parameters. 
2452                      if mo_param == 'dw': 
2453                          self.assertAlmostEqual(set_val/10, min_val/10, 5) 
2454                      elif mo_param == 'kex': 
2455                          self.assertAlmostEqual(set_val/1000, min_val/1000, 5) 
2456                      elif mo_param == 'pA': 
2457                          self.assertAlmostEqual(set_val, min_val, 6) 
2458   
2459   
2460 -    def test_cpmg_synthetic_ns3d_to_cr72_noise_cluster(self): 
2461          """Test synthetic cpmg data. For CR72 with small noise and cluster. 
2462   
2463          This script will produce synthetic CPMG R2eff values according to the selected model, and the fit the selected model. 
2464          """ 
2465   
2466          # Reset. 
2467          #self.interpreter.reset() 
2468   
2469          ## Set Experiments. 
2470          model_create = 'NS CPMG 2-site 3D' 
2471          #model_create = 'NS CPMG 2-site expanded' 
2472          model_analyse = 'CR72' 
2473   
2474          # Exp 1 
2475          sfrq_1 = 599.8908617*1E6 
2476          r20_key_1 = generate_r20_key(exp_type=EXP_TYPE_CPMG_SQ, frq=sfrq_1) 
2477          time_T2_1 = 0.06 
2478          ncycs_1 = [2, 4, 8, 10, 20, 30, 40, 60] 
2479          r2eff_errs_1 = [0.05, -0.05, 0.05, -0.05, 0.05, -0.05, 0.05, -0.05] 
2480          #r2eff_errs_1 = [0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0] 
2481          exp_1 = [sfrq_1, time_T2_1, ncycs_1, r2eff_errs_1] 
2482   
2483          sfrq_2 = 499.8908617*1E6 
2484          r20_key_2 = generate_r20_key(exp_type=EXP_TYPE_CPMG_SQ, frq=sfrq_2) 
2485          time_T2_2 = 0.05 
2486          ncycs_2 = [2, 4, 8, 10, 30, 35, 40, 50] 
2487          r2eff_errs_2 = [0.05, -0.05, 0.05, -0.05, 0.05, -0.05, 0.05, -0.05] 
2488          #r2eff_errs_2 = [0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0] 
2489          exp_2 = [sfrq_2, time_T2_2, ncycs_2, r2eff_errs_2] 
2490   
2491          # Collect all exps 
2492          exps = [exp_1, exp_2] 
2493   
2494          spins = [ 
2495              ['Ala', 1, 'N', {'r2': {r20_key_1:10., r20_key_2:11.5}, 'r2a': {r20_key_1:10., r20_key_2:11.5}, 'r2b': {r20_key_1:10., r20_key_2:11.5}, 'kex': 1000., 'pA': 0.99, 'dw': 2.} ], 
2496              ['Ala', 2, 'N', {'r2': {r20_key_1:13., r20_key_2:14.5}, 'r2a': {r20_key_1:13., r20_key_2:14.5}, 'r2b': {r20_key_1:13., r20_key_2:14.5}, 'kex': 1000., 'pA': 0.99, 'dw': 1.} ] 
2497              ] 
2498   
2499          # Collect the data to be used. 
2500          ds.data = [model_create, model_analyse, spins, exps] 
2501   
2502          # The tmp directory. None is the local directory. 
2503          ds.tmpdir = ds.tmpdir 
2504   
2505          # The results directory. None is the local directory. 
2506          #ds.resdir = None 
2507          ds.resdir = ds.tmpdir 
2508   
2509          # Do r20_from_min_r2eff ?. 
2510          ds.r20_from_min_r2eff = True 
2511   
2512          # Remove insignificant level. 
2513          ds.insignificance = 0.0 
2514   
2515          # The grid search size (the number of increments per dimension). 
2516          ds.GRID_INC = 13 
2517   
2518          # The do clustering. 
2519          ds.do_cluster = True 
2520   
2521          # The function tolerance.  This is used to terminate minimisation once the function value between iterations is less than the tolerance. 
2522          # The default value is 1e-25. 
2523          ds.set_func_tol = 1e-8 
2524   
2525          # The maximum number of iterations. 
2526          # The default value is 1e7. 
2527          ds.set_max_iter = 10000 
2528   
2529          # The verbosity level. 
2530          ds.verbosity = 1 
2531   
2532          # The rel_change WARNING level. 
2533          ds.rel_change = 0.05 
2534   
2535          # The plot_curves. 
2536          ds.plot_curves = False 
2537   
2538          # The conversion for ShereKhan at http://sherekhan.bionmr.org/. 
2539          ds.sherekhan_input = False 
2540   
2541          # Make a dx map to be opened om OpenDX. To map the hypersurface of chi2, when altering kex, dw and pA. 
2542          ds.opendx = False 
2543   
2544          # The set r2eff err. 
2545          ds.r2eff_err = 0.1 
2546   
2547          # The print result info. 
2548          ds.print_res = False 
2549   
2550          # Execute the script. 
2551          self.interpreter.run(script_file=status.install_path + sep+'test_suite'+sep+'system_tests'+sep+'scripts'+sep+'relax_disp'+sep+'cpmg_synthetic.py') 
2552   
2553          cur_spins = ds.data[2] 
2554          # Compare results. 
2555          for i in range(len(cur_spins)): 
2556              res_name, res_num, spin_name, params = cur_spins[i] 
2557              cur_spin_id = ":%i@%s"%(res_num, spin_name) 
2558              cur_spin = return_spin(cur_spin_id) 
2559   
2560              grid_params = ds.grid_results[i][3] 
2561   
2562              # Extract the clust results. 
2563              min_params = ds.clust_results[i][3] 
2564              # Now read the parameters. 
2565              print("For spin: '%s'"%cur_spin_id) 
2566              for mo_param in cur_spin.params: 
2567                  # The R2 is a dictionary, depending on spectrometer frequency. 
2568                  if isinstance(getattr(cur_spin, mo_param), dict): 
2569                      grid_r2 = grid_params[mo_param] 
2570                      min_r2 = min_params[mo_param] 
2571                      set_r2 = params[mo_param] 
2572                      for key, val in set_r2.items(): 
2573                          grid_r2_frq = grid_r2[key] 
2574                          min_r2_frq = min_r2[key] 
2575                          set_r2_frq = set_r2[key] 
2576                          frq = float(key.split(EXP_TYPE_CPMG_SQ+' - ')[-1].split('MHz')[0]) 
2577                          rel_change = math.sqrt( (min_r2_frq - set_r2_frq)**2/(min_r2_frq)**2 ) 
2578                          print("%s %s %s %s %.1f GRID=%.3f MIN=%.3f SET=%.3f RELC=%.3f"%(cur_spin.model, res_name, cur_spin_id, mo_param, frq, grid_r2_frq, min_r2_frq, set_r2_frq, rel_change) ) 
2579                          if rel_change > ds.rel_change: 
2580                              print("WARNING: rel change level is above %.2f, and is %.4f."%(ds.rel_change, rel_change)) 
2581                              print("###################################") 
2582   
2583                          ## Make test on R2. 
2584                          self.assertAlmostEqual(set_r2_frq, min_r2_frq, 1) 
2585                  else: 
2586                      grid_val = grid_params[mo_param] 
2587                      min_val = min_params[mo_param] 
2588                      set_val = params[mo_param] 
2589                      rel_change = math.sqrt( (min_val - set_val)**2/(min_val)**2 ) 
2590                      print("%s %s %s %s GRID=%.3f MIN=%.3f SET=%.3f RELC=%.3f"%(cur_spin.model, res_name, cur_spin_id, mo_param, grid_val, min_val, set_val, rel_change) ) 
2591                      if rel_change > ds.rel_change: 
2592                          print("WARNING: rel change level is above %.2f, and is %.4f."%(ds.rel_change, rel_change)) 
2593                          print("###################################") 
2594   
2595                      ## Make test on parameters. 
2596                      if mo_param == 'dw': 
2597                          self.assertAlmostEqual(set_val/10, min_val/10, 1) 
2598                      elif mo_param == 'kex': 
2599                          self.assertAlmostEqual(set_val/1000, min_val/1000, 1) 
2600                      elif mo_param == 'pA': 
2601                          self.assertAlmostEqual(set_val, min_val, 2) 
2602   
2603   
2604 -    def test_cpmg_synthetic_dx_map_points(self): 
2605          """Test synthetic cpmg data, calling the dx.map function with one or two points. 
2606   
2607          This script will produce synthetic CPMG R2eff values according to the selected model, and the fit the selected model. 
2608          """ 
2609   
2610          # Reset. 
2611          #self.interpreter.reset() 
2612   
2613          ## Set Experiments. 
2614          model_create = MODEL_NS_CPMG_2SITE_EXPANDED 
2615          model_analyse = 'CR72' 
2616          # Exp 1 
2617          sfrq_1 = 599.8908617*1E6 
2618          r20_key_1 = generate_r20_key(exp_type=EXP_TYPE_CPMG_SQ, frq=sfrq_1) 
2619          time_T2_1 = 0.06 
2620          ncycs_1 = [2, 4, 8, 10, 20, 30, 40, 60] 
2621          r2eff_err_1 = [0, 0, 0, 0, 0, 0, 0, 0] 
2622          exp_1 = [sfrq_1, time_T2_1, ncycs_1, r2eff_err_1] 
2623   
2624          sfrq_2 = 499.8908617*1E6 
2625          r20_key_2 = generate_r20_key(exp_type=EXP_TYPE_CPMG_SQ, frq=sfrq_2) 
2626          time_T2_2 = 0.05 
2627          ncycs_2 = [2, 4, 8, 10, 30, 35, 40, 50] 
2628          r2eff_err_2 = [0, 0, 0, 0, 0, 0, 0, 0] 
2629          exp_2 = [sfrq_2, time_T2_2, ncycs_2, r2eff_err_2] 
2630   
2631          # Collect all exps 
2632          exps = [exp_1, exp_2] 
2633   
2634          spins = [ 
2635              ['Ala', 1, 'N', {'r2': {r20_key_1:2, r20_key_2:2}, 'r2a': {r20_key_1:2, r20_key_2:2}, 'r2b': {r20_key_1:2, r20_key_2:2}, 'kex': 1000, 'pA': 0.99, 'dw': 2} ] 
2636              ] 
2637   
2638          # Collect the data to be used. 
2639          ds.data = [model_create, model_analyse, spins, exps] 
2640   
2641          # The tmp directory. None is the local directory. 
2642          ds.tmpdir = ds.tmpdir 
2643   
2644          # The results directory. None is the local directory. 
2645          #ds.resdir = None 
2646          ds.resdir = ds.tmpdir 
2647   
2648          # Do r20_from_min_r2eff ?. 
2649          ds.r20_from_min_r2eff = True 
2650   
2651          # Remove insignificant level. 
2652          ds.insignificance = 0.0 
2653   
2654          # The grid search size (the number of increments per dimension). 
2655          ds.GRID_INC = None 
2656   
2657          # The do clustering. 
2658          ds.do_cluster = False 
2659   
2660          # The function tolerance.  This is used to terminate minimisation once the function value between iterations is less than the tolerance. 
2661          # The default value is 1e-25. 
2662          ds.set_func_tol = 1e-9 
2663   
2664          # The maximum number of iterations. 
2665          # The default value is 1e7. 
2666          ds.set_max_iter = 1000 
2667   
2668          # The verbosity level. 
2669          ds.verbosity = 1 
2670   
2671          # The rel_change WARNING level. 
2672          ds.rel_change = 0.05 
2673   
2674          # The plot_curves. 
2675          ds.plot_curves = False 
2676   
2677          # The conversion for ShereKhan at http://sherekhan.bionmr.org/. 
2678          ds.sherekhan_input = False 
2679   
2680          # Make a dx map to be opened om OpenDX. To map the hypersurface of chi2, when altering kex, dw and pA. 
2681          ds.opendx = False 
2682   
2683          # The set r2eff err. 
2684          ds.r2eff_err = 0.1 
2685   
2686          # The print result info. 
2687          ds.print_res = False 
2688   
2689          # Execute the script. 
2690          self.interpreter.run(script_file=status.install_path + sep+'test_suite'+sep+'system_tests'+sep+'scripts'+sep+'relax_disp'+sep+'cpmg_synthetic.py') 
2691   
2692          # Get the spins. 
2693          cur_spins = ds.data[2] 
2694   
2695          # First switch pipe, since dx.map will go through parameters and end up a "bad" place. :-) 
2696          ds.pipe_name_MODEL_MAP = "%s_%s_map"%(ds.pipe_name, model_analyse) 
2697          self.interpreter.pipe.copy(pipe_from=ds.pipe_name, pipe_to=ds.pipe_name_MODEL_MAP, bundle_to = ds.pipe_bundle) 
2698          self.interpreter.pipe.switch(pipe_name=ds.pipe_name_MODEL_MAP) 
2699   
2700          # Copy R2eff, but not the original parameters 
2701          self.interpreter.value.copy(pipe_from=ds.pipe_name_r2eff, pipe_to=ds.pipe_name_MODEL_MAP, param='r2eff') 
2702   
2703          # Then select model. 
2704          self.interpreter.relax_disp.select_model(model=model_analyse) 
2705   
2706          # Define dx.map settings. 
2707          ds.dx_inc = 4 
2708          ds.dx_params = ['dw', 'pA', 'kex'] 
2709   
2710          res_name, res_num, spin_name, params = cur_spins[0] 
2711          cur_spin_id = ":%i@%s"%(res_num, spin_name) 
2712          cur_spin = return_spin(cur_spin_id) 
2713   
2714          print("Params for dx map is") 
2715          print(ds.dx_params) 
2716          print("Point param for dx map is") 
2717          print(ds.dx_set_val) 
2718          cur_model = model_analyse.replace(' ', '_') 
2719          file_name_map = "%s_map%s" % (cur_model, cur_spin_id.replace('#', '_').replace(':', '_').replace('@', '_')) 
2720          file_name_point = "%s_point%s" % (cur_model, cur_spin_id .replace('#', '_').replace(':', '_').replace('@', '_')) 
2721          self.interpreter.dx.map(params=ds.dx_params, map_type='Iso3D', spin_id=cur_spin_id, inc=ds.dx_inc, lower=None, upper=None, axis_incs=10, file_prefix=file_name_map, dir=ds.resdir, point=[ds.dx_set_val, ds.dx_clust_val], point_file=file_name_point) 
2722   
2723          ## Check for file creation 
2724          # Set filepaths. 
2725          map_cfg = ds.tmpdir+sep+file_name_map+".cfg" 
2726          map_net = ds.tmpdir+sep+file_name_map+".net" 
2727          map_general = ds.tmpdir+sep+file_name_map+".general" 
2728   
2729          point_general = ds.tmpdir+sep+file_name_point+".general" 
2730          point_point = ds.tmpdir+sep+file_name_point 
2731   
2732          # Test the files exists. 
2733          self.assert_(access(map_cfg, F_OK)) 
2734          self.assert_(access(map_net, F_OK)) 
2735          self.assert_(access(map_general, F_OK)) 
2736          self.assert_(access(point_general, F_OK)) 
2737          self.assert_(access(point_point, F_OK)) 
2738   
2739          # Open the files for testing. 
2740          # Check the cfg file. 
2741          print("\nChecking the dx map .cfg file.") 
2742          res_file = [ 
2743              '//'+"\n", 
2744              '//'+"\n", 
2745              '// time: Thu May  8 18:55:31 2014'+"\n", 
2746              '//'+"\n", 
2747              '// version: 3.2.0 (format), 4.3.2 (DX)'+"\n", 
2748              '//'+"\n", 
2749              '//'+"\n", 
2750              '// panel[0]: position = (0.0164,0.0000), size = 0.2521x0.1933, startup = 1, devstyle = 1'+"\n", 
2751              '// title: value = Control Panel'+"\n", 
2752              '//'+"\n", 
2753              '// workspace: width = 251, height = 142'+"\n", 
2754              '// layout: snap = 0, width = 50, height = 50, align = NN'+"\n", 
2755              '//'+"\n", 
2756              '// interactor Selector[1]: num_components = 1, value = 1 '+"\n", 
2757              '// selections: maximum = 2, current = 0 '+"\n", 
2758              '// option[0]: name = "Colour", value = 1'+"\n", 
2759              '// option[1]: name = "Grey", value = 2'+"\n", 
2760              '// instance: panel = 0, x = 81, y = 6, style = Scrolled List, vertical = 1, size = 170x136'+"\n", 
2761              '// label: value = Colour Selector'+"\n", 
2762              '//'+"\n", 
2763              '// node Image[3]:'+"\n", 
2764              '// title: value = Surface'+"\n", 
2765              '// depth: value = 24'+"\n", 
2766              '// window: position = (0.0000,0.0400), size = 0.9929x0.9276'+"\n", 
2767          ] 
2768          file = open(map_cfg, 'r') 
2769          lines = file.readlines() 
2770          file.close() 
2771          for i in range(len(res_file)): 
2772              # Skip time point 
2773              if i == 2: 
2774                  continue 
2775              self.assertEqual(res_file[i], lines[i]) 
2776   
2777          print("\nChecking the dx map .general file.") 
2778          res_file = [ 
2779              'file = CR72_map_1_N'+"\n", 
2780              'grid = 5 x 5 x 5'+"\n", 
2781              'format = ascii'+"\n", 
2782              'interleaving = field'+"\n", 
2783              'majority = row'+"\n", 
2784              'field = data'+"\n", 
2785              'structure = scalar'+"\n", 
2786              'type = float'+"\n", 
2787              'dependency = positions'+"\n", 
2788              'positions = regular, regular, regular, 0, 1, 0, 1, 0, 1'+"\n", 
2789              ''+"\n", 
2790              'end'+"\n", 
2791          ] 
2792          file = open(map_general, 'r') 
2793          lines = file.readlines() 
2794          file.close() 
2795          for i in range(len(res_file)): 
2796              # Skip time point 
2797              #if i == 2: 
2798              #    continue 
2799              self.assertEqual(res_file[i], lines[i]) 
2800   
2801          print("\nChecking the dx point .general file.") 
2802          res_file = [ 
2803              'file = CR72_point_1_N'+"\n", 
2804              'points = 2'+"\n", 
2805              'format = ascii'+"\n", 
2806              'interleaving = field'+"\n", 
2807              'field = locations, field0'+"\n", 
2808              'structure = 3-vector, scalar'+"\n", 
2809              'type = float, float'+"\n", 
2810              ''+"\n", 
2811              'end'+"\n", 
2812          ] 
2813          file = open(point_general, 'r') 
2814          lines = file.readlines() 
2815          file.close() 
2816          for i in range(len(res_file)): 
2817              # Skip time point 
2818              #if i == 2: 
2819              #    continue 
2820              self.assertEqual(res_file[i], lines[i]) 
2821   
2822          print("\nChecking the dx point point file.") 
2823          res_file = [ 
2824              '0.8            3.92           0.39964        1'+"\n", 
2825              '0.76981        3.9169         0.41353        1'+"\n", 
2826          ] 
2827          file = open(point_point, 'r') 
2828          lines = file.readlines() 
2829          file.close() 
2830          for i in range(len(res_file)): 
2831              # Skip time point 
2832              #if i == 2: 
2833              #    continue 
2834              self.assertEqual(res_file[i], lines[i]) 
2835   
2836   
2837 -    def test_curve_type_cpmg_fixed_time(self): 
2838          """Test the curve type detection using the Dr. Flemming Hansen's CPMG fixed time test data.""" 
2839   
2840          # Reset. 
2841          self.interpreter.reset() 
2842   
2843          # Load the base data. 
2844          data_path = status.install_path + sep+'test_suite'+sep+'shared_data'+sep+'dispersion'+sep+'Hansen' 
2845          self.interpreter.state.load(data_path+sep+'r2eff_values') 
2846   
2847          # The type. 
2848          curve_type = get_curve_type(id='500_133.33.in') 
2849          self.assertEqual(curve_type, 'fixed time') 
2850   
2851   
2852 -    def test_curve_type_r1rho_exponential(self, model=None): 
2853          """Test the curve type detection using the 'M61' exponential test data.""" 
2854   
2855          # Reset. 
2856          self.interpreter.reset() 
2857   
2858          # Load the base data. 
2859          data_path = status.install_path + sep+'test_suite'+sep+'shared_data'+sep+'dispersion'+sep+'r1rho_on_res_m61' 
2860          self.interpreter.state.load(data_path+sep+'r2eff_values') 
2861   
2862          # The type. 
2863          curve_type = get_curve_type(id='nu_2000_ncyc9') 
2864          self.assertEqual(curve_type, 'exponential') 
2865   
2866   
2867 -    def test_curve_type_r1rho_fixed_time(self, model=None): 
2868          """Test the curve type detection using the 'TP02' fixed time test data.""" 
2869   
2870          # Reset. 
2871          self.interpreter.reset() 
2872   
2873          # Load the base data. 
2874          data_path = status.install_path + sep+'test_suite'+sep+'shared_data'+sep+'dispersion'+sep+'r1rho_off_res_tp02' 
2875          self.interpreter.state.load(data_path+sep+'r2eff_values') 
2876   
2877          # The type. 
2878          curve_type = get_curve_type(id='nu_1000.0_500MHz') 
2879          self.assertEqual(curve_type, 'fixed time') 
2880   
2881   
2882 -    def test_dpl94_data_to_dpl94(self): 
2883          """Test the relaxation dispersion 'DPL94' model curve fitting to fixed time synthetic data.""" 
2884   
2885          # Fixed time variable. 
2886          ds.fixed = True 
2887   
2888          # Execute the script. 
2889          self.interpreter.run(script_file=status.install_path + sep+'test_suite'+sep+'system_tests'+sep+'scripts'+sep+'relax_disp'+sep+'r1rho_on_res_dpl94.py') 
2890   
2891          # The original parameters. 
2892          i0 = [100000.0, 20000.0] 
2893          r1rho_prime = [2.25, 24.0] 
2894          pA = 0.7 
2895          kex = 1000.0 
2896          delta_omega = [1.0, 2.0] 
2897          phi_ex = [] 
2898          for i in range(2): 
2899              phi_ex.append(pA * (1.0 - pA) * delta_omega[i]**2) 
2900   
2901          # Switch to the 'DPL94' model data pipe, then check for each spin. 
2902          self.interpreter.pipe.switch('DPL94 - relax_disp') 
2903          spin_index = 0 
2904          for spin, spin_id in spin_loop(return_id=True): 
2905              # Printout. 
2906              print("\nSpin %s." % spin_id) 
2907   
2908              # Check the fitted parameters. 
2909              self.assertAlmostEqual(spin.r2['R1rho - 800.00000000 MHz']/10, r1rho_prime[spin_index]/10, 2) 
2910              self.assertAlmostEqual(spin.phi_ex, phi_ex[spin_index], 2) 
2911              self.assertAlmostEqual(spin.kex/1000.0, kex/1000.0, 2) 
2912   
2913              # Increment the spin index. 
2914              spin_index += 1 
2915   
2916   
2917 -    def test_estimate_r2eff_err(self): 
2918          """Test the user function for estimating R2eff errors from exponential curve fitting. 
2919   
2920          This follows Task 7822. 
2921          U{task #7822<https://gna.org/task/index.php?7822>}: Implement user function to estimate R2eff and associated errors for exponential curve fitting. 
2922   
2923          This uses the data from Kjaergaard's paper at U{DOI: 10.1021/bi4001062<http://dx.doi.org/10.1021/bi4001062>}. 
2924          Optimisation of the Kjaergaard et al., 2013 Off-resonance R1rho relaxation dispersion experiments using the 'DPL' model. 
2925          """ 
2926   
2927          # Cluster residues 
2928          cluster_ids = [ 
2929          ":13@N", 
2930          ":15@N", 
2931          ":16@N", 
2932          ":25@N", 
2933          ":26@N", 
2934          ":28@N", 
2935          ":39@N", 
2936          ":40@N", 
2937          ":41@N", 
2938          ":43@N", 
2939          ":44@N", 
2940          ":45@N", 
2941          ":49@N", 
2942          ":52@N", 
2943          ":53@N"] 
2944   
2945          # Load the data. 
2946          self.setup_r1rho_kjaergaard(cluster_ids=cluster_ids, read_R1=False) 
2947   
2948          # The dispersion models. 
2949          MODELS = [MODEL_NOREX, MODEL_DPL94, MODEL_TP02, MODEL_TAP03, MODEL_MP05, MODEL_NS_R1RHO_2SITE] 
2950   
2951          # The grid search size (the number of increments per dimension). 
2952          GRID_INC = None 
2953   
2954          # The number of Monte Carlo simulations to be used for error analysis at the end of the analysis. 
2955          MC_NUM = 3 
2956   
2957          # Model selection technique. 
2958          MODSEL = 'AIC' 
2959   
2960          # Execute the auto-analysis (fast). 
2961          # Standard parameters are: func_tol = 1e-25, grad_tol = None, max_iter = 10000000, 
2962          OPT_FUNC_TOL = 1e-25 
2963          relax_disp.Relax_disp.opt_func_tol = OPT_FUNC_TOL 
2964          OPT_MAX_ITERATIONS = 10000000 
2965          relax_disp.Relax_disp.opt_max_iterations = OPT_MAX_ITERATIONS 
2966   
2967          result_dir_name = ds.tmpdir 
2968   
2969          # Make all spins free 
2970          for curspin in cluster_ids: 
2971              self.interpreter.relax_disp.cluster('free spins', curspin) 
2972              # Shut them down 
2973              self.interpreter.deselect.spin(spin_id=curspin, change_all=False) 
2974   
2975          # Select only a subset of spins for global fitting 
2976          #self.interpreter.select.spin(spin_id=':41@N', change_all=False) 
2977          #self.interpreter.relax_disp.cluster('model_cluster', ':41@N') 
2978   
2979          #self.interpreter.select.spin(spin_id=':40@N', change_all=False) 
2980          #self.interpreter.relax_disp.cluster('model_cluster', ':40@N') 
2981   
2982          self.interpreter.select.spin(spin_id=':52@N', change_all=False) 
2983          #self.interpreter.relax_disp.cluster('model_cluster', ':52@N') 
2984   
2985          # Set the model. 
2986          self.interpreter.relax_disp.select_model(MODEL_R2EFF) 
2987   
2988          # Check if intensity errors have already been calculated. 
2989          check_intensity_errors() 
2990   
2991          # Do a grid search. 
2992          self.interpreter.minimise.grid_search(lower=None, upper=None, inc=11, constraints=True, verbosity=1) 
2993   
2994          # Minimise. 
2995          self.interpreter.minimise.execute(min_algor='Newton', constraints=False, verbosity=1) 
2996   
2997          # Estimate R2eff errors. 
2998          self.interpreter.relax_disp.r2eff_err_estimate() 
2999   
3000          r1_fit = True 
3001   
3002          # Run the analysis. 
3003          relax_disp.Relax_disp(pipe_name=ds.pipe_name, pipe_bundle=ds.pipe_bundle, results_dir=result_dir_name, models=MODELS, grid_inc=GRID_INC, mc_sim_num=MC_NUM, modsel=MODSEL, r1_fit=r1_fit) 
3004   
3005          # Verify the data. 
3006          self.verify_r1rho_kjaergaard_missing_r1(models=MODELS, result_dir_name=result_dir_name, r2eff_estimate='direct') 
3007   
3008   
3009 -    def test_estimate_r2eff_err_auto(self): 
3010          """Test the user function for estimating R2eff errors from exponential curve fitting, via the auto_analyses menu. 
3011   
3012          This follows Task 7822. 
3013          U{task #7822<https://gna.org/task/index.php?7822>}: Implement user function to estimate R2eff and associated errors for exponential curve fitting. 
3014   
3015          This uses the data from Kjaergaard's paper at U{DOI: 10.1021/bi4001062<http://dx.doi.org/10.1021/bi4001062>}. 
3016          Optimisation of the Kjaergaard et al., 2013 Off-resonance R1rho relaxation dispersion experiments using the 'DPL' model. 
3017          """ 
3018   
3019          # Cluster residues 
3020          cluster_ids = [ 
3021          ":13@N", 
3022          ":15@N", 
3023          ":16@N", 
3024          ":25@N", 
3025          ":26@N", 
3026          ":28@N", 
3027          ":39@N", 
3028          ":40@N", 
3029          ":41@N", 
3030          ":43@N", 
3031          ":44@N", 
3032          ":45@N", 
3033          ":49@N", 
3034          ":52@N", 
3035          ":53@N"] 
3036   
3037          # Load the data. 
3038          #self.setup_r1rho_kjaergaard(cluster_ids=cluster_ids, read_R1=False) 
3039          data_path = status.install_path + sep+'test_suite'+sep+'shared_data'+sep+'dispersion'+sep+'Kjaergaard_et_al_2013'+sep 
3040   
3041          # Set pipe name, bundle and type. 
3042          pipe_name = 'base pipe' 
3043          pipe_bundle = 'relax_disp' 
3044          pipe_type = 'relax_disp' 
3045   
3046          # Create the data pipe. 
3047          self.interpreter.pipe.create(pipe_name=pipe_name, bundle=pipe_bundle, pipe_type=pipe_type) 
3048   
3049          file = data_path + '1_setup_r1rho_GUI.py' 
3050          self.interpreter.script(file=file, dir=None) 
3051   
3052          # The dispersion models. 
3053          MODELS = [MODEL_R2EFF, MODEL_NOREX, MODEL_DPL94, MODEL_TP02, MODEL_TAP03, MODEL_MP05, MODEL_NS_R1RHO_2SITE] 
3054   
3055          # The grid search size (the number of increments per dimension). 
3056          GRID_INC = None 
3057   
3058          # The number of Monte Carlo simulations to be used for error analysis for exponential curve fitting of R2eff. 
3059          # When set to minus 1, estimation of the errors will be extracted from the covariance matrix. 
3060          # This is HIGHLY likely to be wrong, but can be used in an initial test fase. 
3061          EXP_MC_NUM = -1 
3062   
3063          # The number of Monte Carlo simulations to be used for error analysis at the end of the analysis. 
3064          MC_NUM = 3 
3065   
3066          # Model selection technique. 
3067          MODSEL = 'AIC' 
3068   
3069          # Execute the auto-analysis (fast). 
3070          # Standard parameters are: func_tol = 1e-25, grad_tol = None, max_iter = 10000000, 
3071          OPT_FUNC_TOL = 1e-25 
3072          relax_disp.Relax_disp.opt_func_tol = OPT_FUNC_TOL 
3073          OPT_MAX_ITERATIONS = 10000000 
3074          relax_disp.Relax_disp.opt_max_iterations = OPT_MAX_ITERATIONS 
3075   
3076          # Make all spins free 
3077          #for curspin in cluster_ids: 
3078          #    self.interpreter.relax_disp.cluster('free spins', curspin) 
3079          #    # Shut them down 
3080          #    self.interpreter.deselect.spin(spin_id=curspin, boolean='OR', change_all=False) 
3081   
3082          # Make all spins free 
3083          self.interpreter.deselect.spin(spin_id=':1-100', change_all=False) 
3084   
3085          # Select only a subset of spins for global fitting 
3086          #self.interpreter.select.spin(spin_id=':41@N', change_all=False) 
3087          #self.interpreter.relax_disp.cluster('model_cluster', ':41@N') 
3088   
3089          #self.interpreter.select.spin(spin_id=':40@N', change_all=False) 
3090          #self.interpreter.relax_disp.cluster('model_cluster', ':40@N') 
3091   
3092          self.interpreter.select.spin(spin_id=':52@N', change_all=False) 
3093          #self.interpreter.relax_disp.cluster('model_cluster', ':52@N') 
3094   
3095          for cur_spin, mol_name, resi, resn, spin_id in spin_loop(full_info=True, return_id=True, skip_desel=True): 
3096              print(spin_id) 
3097   
3098          result_dir_name = self.tmpdir 
3099          r1_fit = True 
3100   
3101          # Run the analysis. 
3102          relax_disp.Relax_disp(pipe_name=pipe_name, pipe_bundle=pipe_bundle, results_dir=result_dir_name, models=MODELS, grid_inc=GRID_INC, mc_sim_num=MC_NUM, exp_mc_sim_num=EXP_MC_NUM, modsel=MODSEL, r1_fit=r1_fit) 
3103   
3104          # Verify the data. 
3105          self.verify_r1rho_kjaergaard_missing_r1(models=MODELS, result_dir_name=result_dir_name, r2eff_estimate='direct') 
3106   
3107   
3108 -    def test_estimate_r2eff_err_methods(self): 
3109          """Test the user function for estimating R2eff and associated errors for exponential curve fitting with different methods. 
3110          This is compared with a run where erros are estimated by 2000 Monte Carlo simulations. 
3111   
3112          This follows Task 7822. 
3113          U{task #7822<https://gna.org/task/index.php?7822>}: Implement user function to estimate R2eff and associated errors for exponential curve fitting. 
3114   
3115          This uses the data from Kjaergaard's paper at U{DOI: 10.1021/bi4001062<http://dx.doi.org/10.1021/bi4001062>}. 
3116          Optimisation of the Kjaergaard et al., 2013 Off-resonance R1rho relaxation dispersion experiments using the 'DPL' model. 
3117   
3118          NOTE: The difference in the methods was due to a bug in relax! 
3119          U{bug #22554<https://gna.org/bugs/index.php?22554>}. The distribution of intensity with errors in Monte-Carlo simulations are markedly more narrow than expected. 
3120   
3121          This dataset is old, and includes 2000 Monte-Carlo simulations, which is performed wrong. 
3122          """ 
3123   
3124          # Define data path. 
3125          prev_data_path = status.install_path + sep+'test_suite'+sep+'shared_data'+sep+'dispersion'+sep+'Kjaergaard_et_al_2013' +sep+ "check_graphs" +sep+ "mc_2000"  +sep+ "R2eff" 
3126   
3127          # Create pipe. 
3128          self.interpreter.pipe.create('MC_2000', 'relax_disp') 
3129   
3130          # Read results for 2000 MC simulations. 
3131          self.interpreter.results.read(prev_data_path + sep + 'results') 
3132   
3133          # Start dic. 
3134          my_dic = {} 
3135          param_key_list = [] 
3136   
3137          # Do boot strapping ? 
3138          do_boot = True 
3139          if do_boot: 
3140              min_algor = 'Newton' 
3141              min_options = () 
3142              sim_boot = 200 
3143              scaling_list = [1.0, 1.0] 
3144   
3145          # First check sim values. 
3146          for cur_spin, mol_name, resi, resn, spin_id in spin_loop(full_info=True, return_id=True, skip_desel=True): 
3147              # Add key to dic. 
3148              my_dic[spin_id] = {} 
3149   
3150              # Loop over sim. 
3151              for i, r2eff_sim in enumerate(cur_spin.r2eff_sim): 
3152                  # Loop over all exp type. 
3153                  for exp_type, frq, offset, point, ei, mi, oi, di in loop_exp_frq_offset_point(return_indices=True): 
3154                      # Generate the param_key. 
3155                      param_key = return_param_key_from_data(exp_type=exp_type, frq=frq, offset=offset, point=point) 
3156                      r2eff_sim_point = r2eff_sim[param_key] 
3157                      i0_sim_point = cur_spin.r2eff_sim[i][param_key] 
3158   
3159                      # Assert point are higher than 0.0. 
3160                      #point_info = "r2eff=%3.2f i0=%3.2f, at %3.1f MHz, for offset=%3.3f ppm and dispersion point %-5.1f, at sim index %i." % (r2eff_sim_point, i0_sim_point, frq/1E6, offset, point, i) 
3161                      #print(point_info) 
3162                      self.assert_(r2eff_sim_point > 0.0) 
3163                      self.assert_(i0_sim_point > 0.0) 
3164   
3165          # Get the data. 
3166          for cur_spin, mol_name, resi, resn, spin_id in spin_loop(full_info=True, return_id=True, skip_desel=True): 
3167              # Generate spin string. 
3168              spin_string = generate_spin_string(spin=cur_spin, mol_name=mol_name, res_num=resi, res_name=resn) 
3169   
3170              for exp_type, frq, offset, point, ei, mi, oi, di in loop_exp_frq_offset_point(return_indices=True): 
3171                  # Generate the param_key. 
3172                  param_key = return_param_key_from_data(exp_type=exp_type, frq=frq, offset=offset, point=point) 
3173   
3174                  # Loop over all sim, and collect data. 
3175                  r2eff_sim_l = [] 
3176                  i0_sim_l = [] 
3177                  for i, r2eff_sim in enumerate(cur_spin.r2eff_sim): 
3178                      i0_sim = cur_spin.i0_sim[i] 
3179   
3180                      r2eff_sim_i = r2eff_sim[param_key] 
3181                      r2eff_sim_l.append(r2eff_sim_i) 
3182                      i0_sim_i = i0_sim[param_key] 
3183                      i0_sim_l.append(i0_sim_i) 
3184   
3185                  # Take the standard deviation of all values. 
3186                  r2eff_sim_err = std(asarray(r2eff_sim_l), ddof=1) 
3187                  i0_sim_err = std(asarray(i0_sim_l), ddof=1) 
3188   
3189                  # Append key. 
3190                  param_key_list.append(param_key) 
3191   
3192                  # Add key to dic. 
3193                  my_dic[spin_id][param_key] = {} 
3194   
3195                  # Get the value. 
3196                  r2eff = getattr(cur_spin, 'r2eff')[param_key] 
3197                  r2eff_err = getattr(cur_spin, 'r2eff_err')[param_key] 
3198                  i0 = getattr(cur_spin, 'i0')[param_key] 
3199                  i0_err = getattr(cur_spin, 'i0_err')[param_key] 
3200   
3201                  # Save to dic. 
3202                  my_dic[spin_id][param_key]['r2eff'] = r2eff 
3203                  my_dic[spin_id][param_key]['r2eff_err'] = r2eff_err 
3204                  my_dic[spin_id][param_key]['i0'] = i0 
3205                  my_dic[spin_id][param_key]['i0_err'] = i0_err 
3206                  my_dic[spin_id][param_key]['r2eff_err_sim'] = r2eff_sim_err 
3207                  my_dic[spin_id][param_key]['i0_err_sim'] = i0_sim_err 
3208   
3209                  # Assert values are equal 
3210                  self.assertAlmostEqual(r2eff_sim_err, r2eff_err) 
3211                  self.assertAlmostEqual(i0_sim_err, i0_err) 
3212   
3213                  if do_boot: 
3214                      values = [] 
3215                      errors = [] 
3216                      times = [] 
3217                      for time in loop_time(exp_type=exp_type, frq=frq, offset=offset, point=point): 
3218                          values.append(average_intensity(spin=cur_spin, exp_type=exp_type, frq=frq, offset=offset, point=point, time=time)) 
3219                          errors.append(average_intensity(spin=cur_spin, exp_type=exp_type, frq=frq, offset=offset, point=point, time=time, error=True)) 
3220                          times.append(time) 
3221   
3222                      # Convert to numpy array. 
3223                      values = asarray(values) 
3224                      errors = asarray(errors) 
3225                      times = asarray(times) 
3226   
3227                      R_m_sim_l = [] 
3228                      I0_m_sim_l = [] 
3229                      for j in range(sim_boot): 
3230                          if j in range(0, 100000, 100): 
3231                              print("Simulation %i"%j) 
3232                          # Start minimisation. 
3233   
3234                          # Produce errors 
3235                          I_err = [] 
3236                          for j, error in enumerate(errors): 
3237                              I_error = gauss(values[j], error) 
3238                              I_err.append(I_error) 
3239                          # Convert to numpy array. 
3240                          I_err = asarray(I_err) 
3241   
3242                          x0 = [r2eff, i0] 
3243                          setup(num_params=len(x0), num_times=len(times), values=I_err, sd=errors, relax_times=times, scaling_matrix=scaling_list) 
3244   
3245                          params_minfx_sim_j, chi2_minfx_sim_j, iter_count, f_count, g_count, h_count, warning = generic_minimise(func=func, dfunc=dfunc, d2func=d2func, args=(), x0=x0, min_algor=min_algor, min_options=min_options, full_output=True, print_flag=0) 
3246                          R_m_sim_j, I0_m_sim_j = params_minfx_sim_j 
3247                          R_m_sim_l.append(R_m_sim_j) 
3248                          I0_m_sim_l.append(I0_m_sim_j) 
3249   
3250                      # Get stats on distribution. 
3251                      sigma_R_sim = std(asarray(R_m_sim_l), ddof=1) 
3252                      sigma_I0_sim = std(asarray(I0_m_sim_l), ddof=1) 
3253                      my_dic[spin_id][param_key]['r2eff_err_boot'] = sigma_R_sim 
3254                      my_dic[spin_id][param_key]['i0_err_boot'] = sigma_I0_sim 
3255   
3256   
3257          # A new data pipe. 
3258          self.interpreter.pipe.copy(pipe_from='MC_2000', pipe_to='r2eff_est') 
3259          self.interpreter.pipe.switch(pipe_name='r2eff_est') 
3260   
3261          # Delete old errors. 
3262          for cur_spin, mol_name, resi, resn, spin_id in spin_loop(full_info=True, return_id=True, skip_desel=True): 
3263              delattr(cur_spin, 'r2eff_err') 
3264              delattr(cur_spin, 'i0_err') 
3265   
3266          # Set the model. 
3267          self.interpreter.relax_disp.select_model(MODEL_R2EFF) 
3268   
3269          # Estimate R2eff and errors. 
3270          self.interpreter.relax_disp.r2eff_err_estimate(verbosity=0) 
3271   
3272          for cur_spin, mol_name, resi, resn, spin_id in spin_loop(full_info=True, return_id=True, skip_desel=True): 
3273              # Generate spin string. 
3274              spin_string = generate_spin_string(spin=cur_spin, mol_name=mol_name, res_num=resi, res_name=resn) 
3275   
3276              for exp_type, frq, offset, point, ei, mi, oi, di in loop_exp_frq_offset_point(return_indices=True): 
3277                  # Generate the param_key. 
3278                  param_key = return_param_key_from_data(exp_type=exp_type, frq=frq, offset=offset, point=point) 
3279   
3280                  # Get the value. 
3281                  r2eff_est = getattr(cur_spin, 'r2eff')[param_key] 
3282                  r2eff_err_est = getattr(cur_spin, 'r2eff_err')[param_key] 
3283                  i0_est = getattr(cur_spin, 'i0')[param_key] 
3284                  i0_err_est = getattr(cur_spin, 'i0_err')[param_key] 
3285   
3286                  # Get from dic. 
3287                  r2eff = my_dic[spin_id][param_key]['r2eff'] 
3288                  r2eff_err = my_dic[spin_id][param_key]['r2eff_err'] 
3289                  i0 = my_dic[spin_id][param_key]['i0'] 
3290                  i0_err = my_dic[spin_id][param_key]['i0_err'] 
3291                  r2eff_sim_err = my_dic[spin_id][param_key]['r2eff_err_sim'] 
3292                  i0_sim_err = my_dic[spin_id][param_key]['i0_err_sim'] 
3293   
3294                  if do_boot: 
3295                      r2eff_boot_err = my_dic[spin_id][param_key]['r2eff_err_boot'] 
3296                      i0_boot_err = my_dic[spin_id][param_key]['i0_err_boot'] 
3297                  else: 
3298                      r2eff_boot_err = 0.0 
3299                      i0_boot_err = 0.0 
3300   
3301                  print("%s at %3.1f MHz, for offset=%3.3f ppm and dispersion point %-5.1f." % (exp_type, frq/1E6, offset, point) ) 
3302                  print("r2eff=%3.3f/%3.3f r2eff_err=%3.4f/%3.4f/%3.4f/%3.4f" % (r2eff, r2eff_est, r2eff_err, r2eff_err_est, r2eff_sim_err, r2eff_boot_err) ), 
3303                  print("i0=%3.3f/%3.3f i0_err=%3.4f/%3.4f/%3.4f/%3.4f\n" % (i0, i0_est, i0_err, i0_err_est, i0_sim_err, i0_boot_err) ) 
3304   
3305   
3306          # Now do it manually. 
3307          estimate_r2eff(method='scipy.optimize.leastsq') 
3308   
3309          estimate_r2eff(method='minfx', min_algor='simplex', c_code=True, constraints=False, chi2_jacobian=False) 
3310          estimate_r2eff(method='minfx', min_algor='simplex', c_code=True, constraints=False, chi2_jacobian=True) 
3311   
3312          estimate_r2eff(method='minfx', min_algor='simplex', c_code=False, constraints=False, chi2_jacobian=False) 
3313          estimate_r2eff(method='minfx', min_algor='simplex', c_code=False, constraints=False, chi2_jacobian=True) 
3314   
3315          estimate_r2eff(method='minfx', min_algor='BFGS', c_code=True, constraints=False, chi2_jacobian=False) 
3316          estimate_r2eff(method='minfx', min_algor='BFGS', c_code=True, constraints=False, chi2_jacobian=True) 
3317   
3318          estimate_r2eff(method='minfx', min_algor='BFGS', c_code=False, constraints=False, chi2_jacobian=False) 
3319          estimate_r2eff(method='minfx', min_algor='BFGS', c_code=False, constraints=False, chi2_jacobian=True) 
3320   
3321          estimate_r2eff(method='minfx', min_algor='Newton', c_code=True, constraints=False, chi2_jacobian=False) 
3322          estimate_r2eff(method='minfx', min_algor='Newton', c_code=True, constraints=False, chi2_jacobian=True) 
3323   
3324   
3325   
3326 -    def test_exp_fit(self): 
3327          """Test the relaxation dispersion 'exp_fit' model curve fitting.""" 
3328   
3329          # Execute the script. 
3330          self.interpreter.run(script_file=status.install_path + sep+'test_suite'+sep+'system_tests'+sep+'scripts'+sep+'relax_disp'+sep+'exp_fit.py') 
3331   
3332          # The original exponential curve parameters. 
3333          res_data = [ 
3334              [15., 10., 20000., 25000.], 
3335              [12., 11., 50000., 51000.], 
3336              [17., 9., 100000., 96000.] 
3337          ] 
3338   
3339          # List of parameters which do not belong to the model. 
3340          blacklist = ['cpmg_frqs', 'r2', 'rex', 'kex', 'r2a', 'k_AB', 'dw'] 
3341   
3342          # Checks for each residue. 
3343          for i in range(len(res_data)): 
3344              # Printout. 
3345              print("\nResidue number %s." % (i+1)) 
3346   
3347              # Check the fitted parameters. 
3348              self.assertAlmostEqual(cdp.mol[0].res[i].spin[0].r2eff['r1rho_1200.00000000_0.000_1000.000'], res_data[i][0], places=2) 
3349              self.assertAlmostEqual(cdp.mol[0].res[i].spin[0].r2eff['r1rho_1200.00000000_0.000_2000.000'], res_data[i][1], places=2) 
3350              self.assertAlmostEqual(cdp.mol[0].res[i].spin[0].i0['r1rho_1200.00000000_0.000_1000.000']/10000, res_data[i][2]/10000, places=3) 
3351              self.assertAlmostEqual(cdp.mol[0].res[i].spin[0].i0['r1rho_1200.00000000_0.000_2000.000']/10000, res_data[i][3]/10000, places=3) 
3352   
3353              # Check the simulation errors. 
3354              self.assert_(cdp.mol[0].res[i].spin[0].r2eff_err['r1rho_1200.00000000_0.000_1000.000'] < 5.0) 
3355              self.assert_(cdp.mol[0].res[i].spin[0].r2eff_err['r1rho_1200.00000000_0.000_2000.000'] < 5.0) 
3356              self.assert_(cdp.mol[0].res[i].spin[0].i0_err['r1rho_1200.00000000_0.000_1000.000']/10000 < 5.0) 
3357              self.assert_(cdp.mol[0].res[i].spin[0].i0_err['r1rho_1200.00000000_0.000_2000.000']/10000 < 5.0) 
3358   
3359              # Check that certain parameters are not present. 
3360              for param in blacklist: 
3361                  print("\tChecking for the absence of the '%s' parameter." % param) 
3362                  self.assert_(not hasattr(cdp.mol[0].res[i].spin[0], param)) 
3363   
3364          # Check the clustering information. 
3365          self.assert_(hasattr(cdp, 'clustering')) 
3366          keys = ['free spins', 'cluster'] 
3367          for key in keys: 
3368              self.assert_(key in cdp.clustering) 
3369          self.assert_('test' not in cdp.clustering) 
3370          self.assertEqual(cdp.clustering['free spins'], [':2@N']) 
3371          self.assertEqual(cdp.clustering['cluster'], [':1@N', ':3@N']) 
3372   
3373   
3374 -    def test_finite_value(self): 
3375          """Test return from C code, when parameters are wrong.  This can happen, if minfx takes a wrong step.""" 
3376   
3377          times = array([ 0.7,  1.,  0.8,  0.4,  0.9]) 
3378          I = array([ 476.76174875,  372.43328777,  454.20339981,  656.87936253,  419.16726341]) 
3379          errors = array([  9.48032653,  11.34093541,   9.35149017,  10.84867928,  12.17590736]) 
3380   
3381          scaling_list = [1.0, 1.0] 
3382          setup(num_params=2, num_times=len(times), values=I, sd=errors, relax_times=times, scaling_matrix=scaling_list) 
3383   
3384          R = - 500. 
3385          I0 = 1000. 
3386          params = [R, I0] 
3387   
3388          chi2 = func(params) 
3389   
3390          print("The chi2 value returned from C-code for R=%3.2f and I0=%3.2f, then chi2=%3.2f"%(R, I0, chi2)) 
3391          self.assertNotEqual(chi2, inf) 
3392   
3393   
3394 -    def test_hansen_catia_input(self): 
3395          """Conversion of Dr. Flemming Hansen's CPMG R2eff values into input files for CATIA. 
3396   
3397          This uses the data from Dr. Flemming Hansen's paper at http://dx.doi.org/10.1021/jp074793o.  This is CPMG data with a fixed relaxation time period. 
3398          """ 
3399   
3400          # Load the R2eff results file. 
3401          file_name = status.install_path + sep+'test_suite'+sep+'shared_data'+sep+'dispersion'+sep+'Hansen'+sep+'r2eff_pipe' 
3402          self.interpreter.results.read(file_name) 
3403          self.interpreter.deselect.spin(':4') 
3404   
3405          # The spin isotopes. 
3406          self.interpreter.spin.isotope("15N") 
3407   
3408          # Generate the input files. 
3409          self.interpreter.relax_disp.catia_input(dir=ds.tmpdir, force=True) 
3410   
3411          # Check the r2eff set files. 
3412          print("\nChecking the R2eff input set files.") 
3413          files = ['data_set_500.inp', 'data_set_500.inp'] 
3414          for file in files: 
3415              self.assert_(access(ds.tmpdir+sep+file, F_OK)) 
3416          data_set_500 = [ 
3417              "ID=500\n", 
3418              "Sfrq = 500\n", 
3419              "Temperature = 0.0\n", 
3420              "Nucleus = N15\n", 
3421              "Couplednucleus = H1\n", 
3422              "Time_equil = 0.0\n", 
3423              "Pwx_cp = 0.0\n", 
3424              "Taub = 0.0\n", 
3425              "Time_T2 = 0.03\n", 
3426              "Xcar = 0.0\n", 
3427              "Seqfil = CW_CPMG\n", 
3428              "Minerror = (2.%;0.5/s)\n", 
3429              "Basis = (Iph_7)\n", 
3430              "Format = (0;1;2)\n", 
3431              "DataDirectory = /tmp/tmpNjOGNG/input_r2eff\n", 
3432              "Data = (\n", 
3433              " [70N;spin_70_N_500.cpmg];\n", 
3434              " [71N;spin_71_N_500.cpmg];\n", 
3435              ")\n", 
3436          ] 
3437          file = open(ds.tmpdir+sep+files[0]) 
3438          lines = file.readlines() 
3439          file.close() 
3440          for i in range(len(data_set_500)): 
3441              # Skip the data directory, as this is a random file name. 
3442              if i == 14: 
3443                  continue 
3444   
3445              self.assertEqual(data_set_500[i], lines[i]) 
3446   
3447          # Check the r2eff files. 
3448          print("\nChecking the R2eff input files.") 
3449          files = ['spin_70_N_500.cpmg', 'spin_70_N_800.cpmg', 'spin_71_N_500.cpmg', 'spin_71_N_800.cpmg'] 
3450          for file in files: 
3451              self.assert_(access(ds.tmpdir+sep+'input_r2eff'+sep+file, F_OK)) 
3452          spin_70_N_500 = [ 
3453              "#        nu_cpmg(Hz)              R2(1/s)              Esd(R2)\n", 
3454              "  66.666600000000003   16.045540885533605    0.310924686180635\n", 
3455              " 133.333300000000008   14.877924861181727    0.303217270671013\n", 
3456              " 200.000000000000000   14.357820247260586    0.299894424543361\n", 
3457              " 266.666600000000017   12.664494620416516    0.289532060485796\n", 
3458              " 333.333300000000008   12.363204802467891    0.287759631749322\n", 
3459              " 400.000000000000000   11.092532381134513    0.280514035409862\n", 
3460              " 466.666600000000017   10.566090057649893    0.277618625949722\n", 
3461              " 533.333300000000008    9.805806894657803    0.273544382200754\n", 
3462              " 600.000000000000000    9.564300692201730    0.272276309984954\n", 
3463              " 666.666600000000017    9.015633750407980    0.269441511838159\n", 
3464              " 733.333300000000008    8.607764958055581    0.267375134391053\n", 
3465              " 800.000000000000000    8.279997179221338    0.265739551961997\n", 
3466              " 866.666600000000017    8.474535940963516    0.266707642726566\n", 
3467              " 933.333300000000008    8.158972897365194    0.265141210539941\n", 
3468              "1000.000000000000000    7.988630509501972    0.264304105548559\n", 
3469          ] 
3470          file = open(ds.tmpdir+sep+'input_r2eff'+sep+files[0]) 
3471          lines = file.readlines() 
3472          file.close() 
3473          for i in range(len(lines)): 
3474              print("%s\"%s\\n\"," % (" "*12, lines[i][:-1])) 
3475          for i in range(len(spin_70_N_500)): 
3476              self.assertEqual(spin_70_N_500[i], lines[i]) 
3477   
3478          # Check the main file. 
3479          print("\nChecking the main CATIA execution file.") 
3480          main_file = [ 
3481              "ReadDataset(data_set_500.inp)\n", 
3482              "ReadDataset(data_set_800.inp)\n", 
3483              "ReadParam_Global(ParamGlobal.inp)\n", 
3484              "ReadParam_Local(ParamSet1.inp)\n", 
3485              "\n", 
3486              "FreeLocalParam(all;Omega;false)\n", 
3487              "FreeLocalParam(all;R1iph_500;false)\n", 
3488              "FreeLocalParam(all;R1iph_800;false)\n", 
3489              "\n", 
3490              "Minimize(print=y;tol=1e-25;maxiter=10000000)\n", 
3491              "\n", 
3492              "PrintParam(output/GlobalParam.fit;global)\n", 
3493              "PrintParam(output/DeltaOmega.fit;DeltaO)\n", 
3494              "PrintData(output/)\n", 
3495              "\n", 
3496              "ChiSq(all;all)\n", 
3497              "exit(0)\n" 
3498          ] 
3499          file = open("%s%sFit.catia" % (ds.tmpdir, sep)) 
3500          lines = file.readlines() 
3501          file.close() 
3502          for i in range(len(main_file)): 
3503              self.assertEqual(main_file[i], lines[i]) 
3504   
3505   
3506 -    def test_hansen_cpmg_data_auto_analysis(self): 
3507          """Test of the dispersion auto-analysis using Dr. Flemming Hansen's CPMG data. 
3508   
3509          This uses the data from Dr. Flemming Hansen's paper at http://dx.doi.org/10.1021/jp074793o.  This is CPMG data with a fixed relaxation time period. 
3510          """ 
3511   
3512          # Set the model. 
3513          ds.models = [ 
3514              MODEL_NOREX, 
3515              MODEL_LM63, 
3516              MODEL_CR72, 
3517              MODEL_IT99 
3518          ] 
3519   
3520          # Execute the script. 
3521          self.interpreter.run(script_file=status.install_path + sep+'test_suite'+sep+'system_tests'+sep+'scripts'+sep+'relax_disp'+sep+'hansen_data.py') 
3522          self.interpreter.state.save('analysis_heights', dir=ds.tmpdir, force=True) 
3523   
3524          # The R20 keys. 
3525          r20_key1 = generate_r20_key(exp_type=EXP_TYPE_CPMG_SQ, frq=500e6) 
3526          r20_key2 = generate_r20_key(exp_type=EXP_TYPE_CPMG_SQ, frq=800e6) 
3527   
3528          # The 'No Rex' model checks. 
3529          self.interpreter.pipe.switch(pipe_name='No Rex - relax_disp') 
3530          spin70 = return_spin(":70") 
3531          spin71 = return_spin(":71") 
3532          print("\n\nOptimised parameters:\n") 
3533          print("%-20s %-20s %-20s" % ("Parameter", "Value (:70)", "Value (:71)")) 
3534          print("%-20s %20.15g %20.15g" % ("R2 (500 MHz)", spin70.r2[r20_key1], spin71.r2[r20_key1])) 
3535          print("%-20s %20.15g %20.15g" % ("R2 (800 MHz)", spin70.r2[r20_key2], spin71.r2[r20_key2])) 
3536          print("%-20s %20.15g %20.15g\n" % ("chi2", spin70.chi2, spin71.chi2)) 
3537          self.assertAlmostEqual(spin70.r2[r20_key1], 10.5340593984683, 3) 
3538          self.assertAlmostEqual(spin70.r2[r20_key2], 16.1112170102734, 3) 
3539          self.assertAlmostEqual(spin70.chi2, 8973.84810025761, 3) 
3540          self.assertAlmostEqual(spin71.r2[r20_key1], 5.83139953954648, 3) 
3541          self.assertAlmostEqual(spin71.r2[r20_key2], 8.90856319376098, 3) 
3542          self.assertAlmostEqual(spin71.chi2, 3908.00127830003, 3) 
3543   
3544          # The 'LM63' model checks. 
3545          self.interpreter.pipe.switch(pipe_name='LM63 - relax_disp') 
3546          spin70 = return_spin(":70") 
3547          spin71 = return_spin(":71") 
3548          print("\n\nOptimised parameters:\n") 
3549          print("%-20s %-20s %-20s" % ("Parameter", "Value (:70)", "Value (:71)")) 
3550          print("%-20s %20.15g %20.15g" % ("R2 (500 MHz)", spin70.r2[r20_key1], spin71.r2[r20_key1])) 
3551          print("%-20s %20.15g %20.15g" % ("R2 (800 MHz)", spin70.r2[r20_key2], spin71.r2[r20_key2])) 
3552          print("%-20s %20.15g %20.15g" % ("phi_ex", spin70.phi_ex, spin71.phi_ex)) 
3553          print("%-20s %20.15g %20.15g" % ("kex", spin70.kex, spin71.kex)) 
3554          print("%-20s %20.15g %20.15g\n" % ("chi2", spin70.chi2, spin71.chi2)) 
3555          self.assertAlmostEqual(spin70.r2[r20_key1], 6.74326615264889, 2) 
3556          self.assertAlmostEqual(spin70.r2[r20_key2], 6.57331164382438, 2) 
3557          self.assertAlmostEqual(spin70.phi_ex, 0.312767653822936, 3) 
3558          self.assertAlmostEqual(spin70.kex/10000, 4723.44390412119/10000, 3) 
3559          self.assertAlmostEqual(spin70.chi2, 363.534049046805, 3) 
3560          self.assertAlmostEqual(spin71.r2[r20_key1], 5.00778024769786, 3) 
3561          self.assertAlmostEqual(spin71.r2[r20_key2], 6.83343630016037, 3) 
3562          self.assertAlmostEqual(spin71.phi_ex, 0.0553791362097596, 3) 
3563          self.assertAlmostEqual(spin71.kex/10000, 2781.67925957068/10000, 3) 
3564          self.assertAlmostEqual(spin71.chi2, 17.0776426190574, 3) 
3565   
3566          # The 'CR72' model checks. 
3567          self.interpreter.pipe.switch(pipe_name='CR72 - relax_disp') 
3568          spin70 = return_spin(":70") 
3569          spin71 = return_spin(":71") 
3570          print("\n\nOptimised parameters:\n") 
3571          print("%-20s %-20s %-20s" % ("Parameter", "Value (:70)", "Value (:71)")) 
3572          print("%-20s %20.15g %20.15g" % ("R2 (500 MHz)", spin70.r2[r20_key1], spin71.r2[r20_key1])) 
3573          print("%-20s %20.15g %20.15g" % ("R2 (800 MHz)", spin70.r2[r20_key2], spin71.r2[r20_key2])) 
3574          print("%-20s %20.15g %20.15g" % ("pA", spin70.pA, spin71.pA)) 
3575          print("%-20s %20.15g %20.15g" % ("dw", spin70.dw, spin71.dw)) 
3576          print("%-20s %20.15g %20.15g" % ("kex", spin70.kex, spin71.kex)) 
3577          print("%-20s %20.15g %20.15g\n" % ("chi2", spin70.chi2, spin71.chi2)) 
3578          self.assertAlmostEqual(spin70.r2[r20_key1], 6.97233943292193, 3) 
3579          self.assertAlmostEqual(spin70.r2[r20_key2], 9.409506394526, 2) 
3580          self.assertAlmostEqual(spin70.pA, 0.989856804525044, 3) 
3581          self.assertAlmostEqual(spin70.dw, 5.60889078920945, 3) 
3582          self.assertAlmostEqual(spin70.kex/10000, 1753.01607073019/10000, 3) 
3583          self.assertAlmostEqual(spin70.chi2, 53.8382158551706, 3) 
3584          self.assertAlmostEqual(spin71.r2[r20_key1], 5.003171547206, 3) 
3585          self.assertAlmostEqual(spin71.r2[r20_key2], 6.90210797727492, 3) 
3586          self.assertAlmostEqual(spin71.pA, 0.985922406455826, 3) 
3587          self.assertAlmostEqual(spin71.dw, 2.00500965892672, 2) 
3588          self.assertAlmostEqual(spin71.kex/10000, 2481.10839579617/10000, 3) 
3589          self.assertAlmostEqual(spin71.chi2, 15.6595374286822, 3) 
3590   
3591   
3592 -    def test_hansen_cpmg_data_auto_analysis_numeric(self): 
3593          """Test of the numeric model only dispersion auto-analysis using Dr. Flemming Hansen's CPMG data. 
3594   
3595          This uses the data from Dr. Flemming Hansen's paper at http://dx.doi.org/10.1021/jp074793o.  This is CPMG data with a fixed relaxation time period. 
3596          """ 
3597   
3598          # Set the model and numeric flag. 
3599          ds.models = [ 
3600              MODEL_NOREX, 
3601              MODEL_CR72, 
3602              MODEL_NS_CPMG_2SITE_EXPANDED 
3603          ] 
3604          ds.numeric_only = True 
3605   
3606          # Execute the script. 
3607          self.interpreter.run(script_file=status.install_path + sep+'test_suite'+sep+'system_tests'+sep+'scripts'+sep+'relax_disp'+sep+'hansen_data.py') 
3608   
3609          # The R20 keys. 
3610          r20_key1 = generate_r20_key(exp_type=EXP_TYPE_CPMG_SQ, frq=500e6) 
3611          r20_key2 = generate_r20_key(exp_type=EXP_TYPE_CPMG_SQ, frq=800e6) 
3612   
3613          # The 'No Rex' model checks. 
3614          self.interpreter.pipe.switch(pipe_name='No Rex - relax_disp') 
3615          spin70 = return_spin(":70") 
3616          spin71 = return_spin(":71") 
3617          print("\n\nOptimised parameters:\n") 
3618          print("%-20s %-20s %-20s" % ("Parameter", "Value (:70)", "Value (:71)")) 
3619          print("%-20s %20.15g %20.15g" % ("R2 (500 MHz)", spin70.r2[r20_key1], spin71.r2[r20_key1])) 
3620          print("%-20s %20.15g %20.15g" % ("R2 (800 MHz)", spin70.r2[r20_key2], spin71.r2[r20_key2])) 
3621          print("%-20s %20.15g %20.15g\n" % ("chi2", spin70.chi2, spin71.chi2)) 
3622          self.assertAlmostEqual(spin70.r2[r20_key1], 10.5340593984683, 3) 
3623          self.assertAlmostEqual(spin70.r2[r20_key2], 16.1112170102734, 3) 
3624          self.assertAlmostEqual(spin70.chi2/10000, 8973.84810025761/10000, 3) 
3625          self.assertAlmostEqual(spin71.r2[r20_key1], 5.83139953954648, 3) 
3626          self.assertAlmostEqual(spin71.r2[r20_key2], 8.90856319376098, 3) 
3627          self.assertAlmostEqual(spin71.chi2/10000, 3908.00127830003/10000, 3) 
3628   
3629          # The 'CR72' model checks. 
3630          self.interpreter.pipe.switch(pipe_name='CR72 - relax_disp') 
3631          spin70 = return_spin(":70") 
3632          spin71 = return_spin(":71") 
3633          print("\n\nOptimised parameters:\n") 
3634          print("%-20s %-20s %-20s" % ("Parameter", "Value (:70)", "Value (:71)")) 
3635          print("%-20s %20.15g %20.15g" % ("R2 (500 MHz)", spin70.r2[r20_key1], spin71.r2[r20_key1])) 
3636          print("%-20s %20.15g %20.15g" % ("R2 (800 MHz)", spin70.r2[r20_key2], spin71.r2[r20_key2])) 
3637          print("%-20s %20.15g %20.15g" % ("pA", spin70.pA, spin71.pA)) 
3638          print("%-20s %20.15g %20.15g" % ("dw", spin70.dw, spin71.dw)) 
3639          print("%-20s %20.15g %20.15g" % ("kex", spin70.kex, spin71.kex)) 
3640          print("%-20s %20.15g %20.15g\n" % ("chi2", spin70.chi2, spin71.chi2)) 
3641          self.assertAlmostEqual(spin70.r2[r20_key1], 6.97233943292193, 3) 
3642          self.assertAlmostEqual(spin70.r2[r20_key2], 9.409506394526, 2) 
3643          self.assertAlmostEqual(spin70.pA, 0.989856804525044, 3) 
3644          self.assertAlmostEqual(spin70.dw, 5.60889078920945, 3) 
3645          self.assertAlmostEqual(spin70.kex/10000, 1753.01607073019/10000, 3) 
3646          self.assertAlmostEqual(spin70.chi2, 53.8382158551706, 3) 
3647          self.assertAlmostEqual(spin71.r2[r20_key1], 5.003171547206, 3) 
3648          self.assertAlmostEqual(spin71.r2[r20_key2], 6.90210797727492, 3) 
3649          self.assertAlmostEqual(spin71.pA, 0.985922406455826, 3) 
3650          self.assertAlmostEqual(spin71.dw, 2.00500965892672, 2) 
3651          self.assertAlmostEqual(spin71.kex/10000, 2481.10839579617/10000, 3) 
3652          self.assertAlmostEqual(spin71.chi2, 15.6595374286822, 3) 
3653   
3654          # The 'NS CPMG 2-site expanded' model checks. 
3655          self.interpreter.pipe.switch(pipe_name='NS CPMG 2-site expanded - relax_disp') 
3656          spin70 = return_spin(":70") 
3657          spin71 = return_spin(":71") 
3658          print("\n\nOptimised parameters:\n") 
3659          print("%-20s %-20s %-20s" % ("Parameter", "Value (:70)", "Value (:71)")) 
3660          print("%-20s %20.15g %20.15g" % ("R2 (500 MHz)", spin70.r2[r20_key1], spin71.r2[r20_key1])) 
3661          print("%-20s %20.15g %20.15g" % ("R2 (800 MHz)", spin70.r2[r20_key2], spin71.r2[r20_key2])) 
3662          print("%-20s %20.15g %20.15g" % ("pA", spin70.pA, spin71.pA)) 
3663          print("%-20s %20.15g %20.15g" % ("dw", spin70.dw, spin71.dw)) 
3664          print("%-20s %20.15g %20.15g" % ("kex", spin70.kex, spin71.kex)) 
3665          print("%-20s %20.15g %20.15g\n" % ("chi2", spin70.chi2, spin71.chi2)) 
3666          self.assertAlmostEqual(spin70.r2[r20_key1], 6.95815351460902, 3) 
3667          self.assertAlmostEqual(spin70.r2[r20_key2], 9.39649535771294, 3) 
3668          self.assertAlmostEqual(spin70.pA, 0.989701014493195, 3) 
3669          self.assertAlmostEqual(spin70.dw, 5.67314464776128, 3) 
3670          self.assertAlmostEqual(spin70.kex/10000, 1713.65380495429/10000, 3) 
3671          self.assertAlmostEqual(spin70.chi2, 52.5106880917473, 3) 
3672          self.assertAlmostEqual(spin71.r2[r20_key1], 4.99889337382435, 3) 
3673          self.assertAlmostEqual(spin71.r2[r20_key2], 6.89822887466673, 3) 
3674          self.assertAlmostEqual(spin71.pA, 0.986709050819695, 3) 
3675          self.assertAlmostEqual(spin71.dw, 2.09238266766502, 2) 
3676          self.assertAlmostEqual(spin71.kex/10000, 2438.27019901422/10000, 3) 
3677          self.assertAlmostEqual(spin71.chi2, 15.1644906963987, 3) 
3678   
3679          # The final data pipe checks. 
3680          self.interpreter.pipe.switch(pipe_name='final - relax_disp') 
3681          spin70 = return_spin(":70") 
3682          spin71 = return_spin(":71") 
3683          self.assertEqual(spin70.model, 'NS CPMG 2-site expanded') 
3684          self.assertEqual(spin71.model, 'NS CPMG 2-site expanded') 
3685   
3686   
3687 -    def test_hansen_cpmg_data_auto_analysis_r2eff(self): 
3688          """Test of the dispersion auto-analysis using Dr. Flemming Hansen's CPMG data (using the R2eff data directly instead of peak intensities). 
3689   
3690          This uses the data from Dr. Flemming Hansen's paper at http://dx.doi.org/10.1021/jp074793o.  This is CPMG data with a fixed relaxation time period. 
3691          """ 
3692   
3693          # Set the model. 
3694          ds.models = [ 
3695              MODEL_NOREX, 
3696              MODEL_LM63, 
3697              MODEL_CR72, 
3698              MODEL_IT99 
3699          ] 
3700   
3701          # Execute the script. 
3702          self.interpreter.run(script_file=status.install_path + sep+'test_suite'+sep+'system_tests'+sep+'scripts'+sep+'relax_disp'+sep+'hansen_r2eff_data.py') 
3703          self.interpreter.state.save('analysis_r2eff', dir=ds.tmpdir, force=True) 
3704   
3705          # The R20 keys. 
3706          r20_key1 = generate_r20_key(exp_type=EXP_TYPE_CPMG_SQ, frq=500e6) 
3707          r20_key2 = generate_r20_key(exp_type=EXP_TYPE_CPMG_SQ, frq=800e6) 
3708   
3709          # The 'No Rex' model checks. 
3710          self.interpreter.pipe.switch(pipe_name='No Rex - relax_disp') 
3711          spin70 = return_spin(":70") 
3712          spin71 = return_spin(":71") 
3713          print("\n\nOptimised parameters:\n") 
3714          print("%-20s %-20s %-20s" % ("Parameter", "Value (:70)", "Value (:71)")) 
3715          print("%-20s %20.15g %20.15g" % ("R2 (500 MHz)", spin70.r2[r20_key1], spin71.r2[r20_key1])) 
3716          print("%-20s %20.15g %20.15g" % ("R2 (800 MHz)", spin70.r2[r20_key2], spin71.r2[r20_key2])) 
3717          print("%-20s %20.15g %20.15g\n" % ("chi2", spin70.chi2, spin71.chi2)) 
3718          self.assertAlmostEqual(spin70.r2[r20_key1], 10.5340593984683, 3) 
3719          self.assertAlmostEqual(spin70.r2[r20_key2], 16.1112170102734, 3) 
3720          self.assertAlmostEqual(spin70.chi2, 8973.84810025761, 3) 
3721          self.assertAlmostEqual(spin71.r2[r20_key1], 5.83139953954648, 3) 
3722          self.assertAlmostEqual(spin71.r2[r20_key2], 8.90856319376098, 3) 
3723          self.assertAlmostEqual(spin71.chi2, 3908.00127830003, 3) 
3724   
3725          # The 'LM63' model checks. 
3726          self.interpreter.pipe.switch(pipe_name='LM63 - relax_disp') 
3727          spin70 = return_spin(":70") 
3728          spin71 = return_spin(":71") 
3729          print("\n\nOptimised parameters:\n") 
3730          print("%-20s %-20s %-20s" % ("Parameter", "Value (:70)", "Value (:71)")) 
3731          print("%-20s %20.15g %20.15g" % ("R2 (500 MHz)", spin70.r2[r20_key1], spin71.r2[r20_key1])) 
3732          print("%-20s %20.15g %20.15g" % ("R2 (800 MHz)", spin70.r2[r20_key2], spin71.r2[r20_key2])) 
3733          print("%-20s %20.15g %20.15g" % ("phi_ex", spin70.phi_ex, spin71.phi_ex)) 
3734          print("%-20s %20.15g %20.15g" % ("kex", spin70.kex, spin71.kex)) 
3735          print("%-20s %20.15g %20.15g\n" % ("chi2", spin70.chi2, spin71.chi2)) 
3736          self.assertAlmostEqual(spin70.r2[r20_key1], 6.74326615264889, 2) 
3737          self.assertAlmostEqual(spin70.r2[r20_key2], 6.57331164382438, 2) 
3738          self.assertAlmostEqual(spin70.phi_ex, 0.312767653822936, 3) 
3739          self.assertAlmostEqual(spin70.kex/10000, 4723.44390412119/10000, 3) 
3740          self.assertAlmostEqual(spin70.chi2, 363.534049046805, 3) 
3741          self.assertAlmostEqual(spin71.r2[r20_key1], 5.00778024769786, 3) 
3742          self.assertAlmostEqual(spin71.r2[r20_key2], 6.83343630016037, 3) 
3743          self.assertAlmostEqual(spin71.phi_ex, 0.0553791362097596, 3) 
3744          self.assertAlmostEqual(spin71.kex/10000, 2781.67925957068/10000, 3) 
3745          self.assertAlmostEqual(spin71.chi2, 17.0776426190574, 3) 
3746   
3747          # The 'CR72' model checks. 
3748          self.interpreter.pipe.switch(pipe_name='CR72 - relax_disp') 
3749          spin70 = return_spin(":70") 
3750          spin71 = return_spin(":71") 
3751          print("\n\nOptimised parameters:\n") 
3752          print("%-20s %-20s %-20s" % ("Parameter", "Value (:70)", "Value (:71)")) 
3753          print("%-20s %20.15g %20.15g" % ("R2 (500 MHz)", spin70.r2[r20_key1], spin71.r2[r20_key1])) 
3754          print("%-20s %20.15g %20.15g" % ("R2 (800 MHz)", spin70.r2[r20_key2], spin71.r2[r20_key2])) 
3755          print("%-20s %20.15g %20.15g" % ("pA", spin70.pA, spin71.pA)) 
3756          print("%-20s %20.15g %20.15g" % ("dw", spin70.dw, spin71.dw)) 
3757          print("%-20s %20.15g %20.15g" % ("kex", spin70.kex, spin71.kex)) 
3758          print("%-20s %20.15g %20.15g\n" % ("chi2", spin70.chi2, spin71.chi2)) 
3759          self.assertAlmostEqual(spin70.r2[r20_key1], 6.97233943292193, 3) 
3760          self.assertAlmostEqual(spin70.r2[r20_key2], 9.409506394526, 2) 
3761          self.assertAlmostEqual(spin70.pA, 0.989856804525044, 3) 
3762          self.assertAlmostEqual(spin70.dw, 5.60889078920945, 3) 
3763          self.assertAlmostEqual(spin70.kex/10000, 1753.01607073019/10000, 3) 
3764          self.assertAlmostEqual(spin70.chi2, 53.8382158551706, 3) 
3765          self.assertAlmostEqual(spin71.r2[r20_key1], 5.00317154730225, 3) 
3766          self.assertAlmostEqual(spin71.r2[r20_key2], 6.90210797713541, 3) 
3767          self.assertAlmostEqual(spin71.pA, 0.985922406429147, 3) 
3768          self.assertAlmostEqual(spin71.dw, 2.00500965887772, 2) 
3769          self.assertAlmostEqual(spin71.kex/10000, 2481.10839579804/10000, 3) 
3770          self.assertAlmostEqual(spin71.chi2, 15.6595374288635, 3) 
3771   
3772   
3773 -    def test_hansen_cpmg_data_missing_auto_analysis(self): 
3774          """Test of the dispersion auto-analysis using Dr. Flemming Hansen's CPMG data with parts missing. 
3775   
3776          This uses the data from Dr. Flemming Hansen's paper at http://dx.doi.org/10.1021/jp074793o.  This is CPMG data with a fixed relaxation time period. 
3777          """ 
3778   
3779          # Set the model. 
3780          ds.models = [ 
3781              MODEL_R2EFF, 
3782              MODEL_NOREX, 
3783              MODEL_CR72, 
3784              MODEL_NS_CPMG_2SITE_EXPANDED 
3785          ] 
3786   
3787          # Execute the script. 
3788          self.interpreter.run(script_file=status.install_path + sep+'test_suite'+sep+'system_tests'+sep+'scripts'+sep+'relax_disp'+sep+'hansen_data_missing.py') 
3789          self.interpreter.state.save('analysis_heights', dir=ds.tmpdir, force=True) 
3790   
3791          # The R20 keys. 
3792          r20_key1 = generate_r20_key(exp_type=EXP_TYPE_CPMG_SQ, frq=500e6) 
3793          r20_key2 = generate_r20_key(exp_type=EXP_TYPE_CPMG_SQ, frq=800e6) 
3794   
3795          # The 'No Rex' model checks. 
3796          self.interpreter.pipe.switch(pipe_name='No Rex - relax_disp') 
3797          spin4 = return_spin(":4") 
3798          spin70 = return_spin(":70") 
3799          spin71 = return_spin(":71") 
3800          print("\n\nOptimised parameters:\n") 
3801          print("%-20s %-20s %-20s %-20s" % ("Parameter", "Value (:4)", "Value (:70)", "Value (:71)")) 
3802          print("%-20s %20.15g %20.15g %20.15g" % ("R2 (500 MHz)", spin4.r2[r20_key1], spin70.r2[r20_key1], spin71.r2[r20_key1])) 
3803          print("%-20s %20.15g %20.15g %20.15g" % ("R2 (800 MHz)", spin4.r2[r20_key2], spin70.r2[r20_key2], spin71.r2[r20_key2])) 
3804          print("%-20s %20.15g %20.15g %20.15g\n" % ("chi2", spin4.chi2, spin70.chi2, spin71.chi2)) 
3805          self.assertAlmostEqual(spin4.r2[r20_key1], 1.60463084515171, 3) 
3806          self.assertAlmostEqual(spin4.r2[r20_key2], 1.63220784651911, 3) 
3807          self.assertAlmostEqual(spin4.chi2, 26.7356700694891, 3) 
3808          self.assertAlmostEqual(spin70.r2[r20_key1], 10.534285641325, 3) 
3809          self.assertAlmostEqual(spin70.r2[r20_key2], 16.1112794857068, 3) 
3810          self.assertAlmostEqual(spin70.chi2, 8973.84809774722, 3) 
3811          self.assertAlmostEqual(spin71.r2[r20_key1], 5.83136858890037, 3) 
3812          self.assertAlmostEqual(spin71.chi2, 182.60081909193, 3) 
3813   
3814          # The 'CR72' model checks. 
3815          self.interpreter.pipe.switch(pipe_name='CR72 - relax_disp') 
3816          spin4 = return_spin(":4") 
3817          spin70 = return_spin(":70") 
3818          spin71 = return_spin(":71") 
3819          print("\n\nOptimised parameters:\n") 
3820          print("%-20s %-20s %-20s %-20s" % ("Parameter", "Value (:4)", "Value (:70)", "Value (:71)")) 
3821          print("%-20s %20.15g %20.15g %20.15g" % ("R2 (500 MHz)", spin4.r2[r20_key1], spin70.r2[r20_key1], spin71.r2[r20_key1])) 
3822          print("%-20s %20.15g %20.15g %20.15g" % ("R2 (800 MHz)", spin4.r2[r20_key2], spin70.r2[r20_key2], spin71.r2[r20_key2])) 
3823          print("%-20s %20.15g %20.15g %20.15g" % ("pA", spin4.pA, spin70.pA, spin71.pA)) 
3824          print("%-20s %20.15g %20.15g %20.15g" % ("dw", spin4.dw, spin70.dw, spin71.dw)) 
3825          print("%-20s %20.15g %20.15g %20.15g" % ("kex", spin4.kex, spin70.kex, spin71.kex)) 
3826          print("%-20s %20.15g %20.15g %20.15g\n" % ("chi2", spin4.chi2, spin70.chi2, spin71.chi2)) 
3827          self.assertAlmostEqual(spin4.r2[r20_key1], 1.60463650370664, 2) 
3828          self.assertAlmostEqual(spin4.r2[r20_key2], 1.63221675941434, 3) 
3829          #self.assertAlmostEqual(spin4.pA, 0.818979078699935, 3)    # As dw (and kex) is zero, this parameter is not stable. 
3830          self.assertAlmostEqual(spin4.dw, 0.0, 5) 
3831          self.assertAlmostEqual(spin4.kex/10000, 0.0, 3) 
3832          self.assertAlmostEqual(spin4.chi2/100, 26.7356711142038/100, 3) 
3833          self.assertAlmostEqual(spin70.r2[r20_key1], 6.97268077496405, 3) 
3834          self.assertAlmostEqual(spin70.r2[r20_key2], 9.41028133407727, 3) 
3835          self.assertAlmostEqual(spin70.pA, 0.989856641885939, 3) 
3836          self.assertAlmostEqual(spin70.dw, 5.60889911049405, 3) 
3837          self.assertAlmostEqual(spin70.kex/10000, 1752.62025618632/10000, 3) 
3838          self.assertAlmostEqual(spin70.chi2, 53.8382196964083, 3) 
3839          self.assertAlmostEqual(spin71.r2[r20_key1], 4.98123328466942, 3) 
3840          self.assertAlmostEqual(spin71.pA, 0.996607425484157, 3) 
3841          self.assertAlmostEqual(spin71.dw, 4.34346257383825, 3) 
3842          self.assertAlmostEqual(spin71.kex/10000, 1936.73197158804/10000, 3) 
3843          self.assertAlmostEqual(spin71.chi2, 5.51703791653689, 3) 
3844   
3845   
3846 -    def test_hansen_cpmg_data_to_cr72(self): 
3847          """Optimisation of Dr. Flemming Hansen's CPMG data to the CR72 dispersion model. 
3848   
3849          This uses the data from Dr. Flemming Hansen's paper at http://dx.doi.org/10.1021/jp074793o.  This is CPMG data with a fixed relaxation time period. 
3850          """ 
3851   
3852          # Base data setup. 
3853          self.setup_hansen_cpmg_data(model='CR72') 
3854   
3855          # Alias the spins. 
3856          spin70 = return_spin(":70") 
3857          spin71 = return_spin(":71") 
3858   
3859          # The R20 keys. 
3860          r20_key1 = generate_r20_key(exp_type=EXP_TYPE_CPMG_SQ, frq=500e6) 
3861          r20_key2 = generate_r20_key(exp_type=EXP_TYPE_CPMG_SQ, frq=800e6) 
3862   
3863          # Set the initial parameter values. 
3864          spin70.r2 = {r20_key1: 7.0, r20_key2: 9.0} 
3865          spin70.pA = 0.9 
3866          spin70.dw = 6.0 
3867          spin70.kex = 1500.0 
3868          spin71.r2 = {r20_key1: 5, r20_key2: 9.0} 
3869          spin71.pA = 0.9 
3870          spin71.dw = 4.0 
3871          spin71.kex = 1900.0 
3872   
3873          # Low precision optimisation. 
3874          self.interpreter.minimise.execute(min_algor='simplex', line_search=None, hessian_mod=None, hessian_type=None, func_tol=1e-05, grad_tol=None, max_iter=1000, constraints=True, scaling=True, verbosity=1) 
3875   
3876          # Printout. 
3877          print("\n\nOptimised parameters:\n") 
3878          print("%-20s %-20s %-20s" % ("Parameter", "Value (:70)", "Value (:71)")) 
3879          print("%-20s %20.15g %20.15g" % ("R2 (500 MHz)", spin70.r2[r20_key1], spin71.r2[r20_key1])) 
3880          print("%-20s %20.15g %20.15g" % ("R2 (800 MHz)", spin70.r2[r20_key2], spin71.r2[r20_key2])) 
3881          print("%-20s %20.15g %20.15g" % ("pA", spin70.pA, spin71.pA)) 
3882          print("%-20s %20.15g %20.15g" % ("dw", spin70.dw, spin71.dw)) 
3883          print("%-20s %20.15g %20.15g" % ("kex", spin70.kex, spin71.kex)) 
3884          print("%-20s %20.15g %20.15g\n" % ("chi2", spin70.chi2, spin71.chi2)) 
3885   
3886          # Checks for residue :70. 
3887          self.assertAlmostEqual(spin70.r2[r20_key1], 6.9724581325007, 4) 
3888          self.assertAlmostEqual(spin70.r2[r20_key2], 9.40968331038162, 2) 
3889          self.assertAlmostEqual(spin70.pA, 0.989856656702431, 4) 
3890          self.assertAlmostEqual(spin70.dw, 5.60885879594746, 3) 
3891          self.assertAlmostEqual(spin70.kex/1000, 1752.91052702273/1000, 3) 
3892          self.assertAlmostEqual(spin70.chi2, 53.8382133597495, 4) 
3893   
3894          # Checks for residue :71. 
3895          self.assertAlmostEqual(spin71.r2[r20_key1], 5.0030740940524, 4) 
3896          self.assertAlmostEqual(spin71.pA, 0.985941082507823, 4) 
3897          self.assertAlmostEqual(spin71.dw, 2.00640384113696, 4) 
3898          self.assertAlmostEqual(spin71.kex/1000, 2480.79614442041/1000, 4) 
3899          self.assertAlmostEqual(spin71.chi2, 15.6595388312451, 4) 
3900   
3901          # Test the conversion to k_AB from kex and pA. 
3902          self.assertEqual(spin70.k_AB, spin70.kex * (1.0 - spin70.pA)) 
3903          self.assertEqual(spin71.k_AB, spin71.kex * (1.0 - spin71.pA)) 
3904   
3905          # Test the conversion to k_BA from kex and pA. 
3906          self.assertEqual(spin70.k_BA, spin70.kex * spin70.pA) 
3907          self.assertEqual(spin71.k_BA, spin71.kex * spin71.pA) 
3908   
3909   
3910 -    def test_hansen_cpmg_data_to_cr72_full(self): 
3911          """Optimisation of Dr. Flemming Hansen's CPMG data to the CR72 full dispersion model. 
3912   
3913          This uses the data from Dr. Flemming Hansen's paper at http://dx.doi.org/10.1021/jp074793o.  This is CPMG data with a fixed relaxation time period. 
3914          """ 
3915   
3916          # Base data setup. 
3917          self.setup_hansen_cpmg_data(model='CR72 full') 
3918   
3919          # Alias the spins. 
3920          spin70 = return_spin(":70") 
3921          spin71 = return_spin(":71") 
3922   
3923          # The R20 keys. 
3924          r20_key1 = generate_r20_key(exp_type=EXP_TYPE_CPMG_SQ, frq=500e6) 
3925          r20_key2 = generate_r20_key(exp_type=EXP_TYPE_CPMG_SQ, frq=800e6) 
3926   
3927          # Set the initial parameter values. 
3928          spin70.r2a = {r20_key1: 7.0, r20_key2: 9.0} 
3929          spin70.r2b = {r20_key1: 7.0, r20_key2: 9.0} 
3930          spin70.pA = 0.9 
3931          spin70.dw = 6.0 
3932          spin70.kex = 1500.0 
3933          spin71.r2a = {r20_key1: 5.0, r20_key2: 9.0} 
3934          spin71.r2b = {r20_key1: 5.0, r20_key2: 9.0} 
3935          spin71.pA = 0.9 
3936          spin71.dw = 4.0 
3937          spin71.kex = 1900.0 
3938   
3939          # Low precision optimisation. 
3940          self.interpreter.minimise.execute(min_algor='simplex', line_search=None, hessian_mod=None, hessian_type=None, func_tol=1e-05, grad_tol=None, max_iter=1000, constraints=True, scaling=True, verbosity=1) 
3941   
3942          # Printout. 
3943          print("\n\nOptimised parameters:\n") 
3944          print("%-20s %-20s %-20s" % ("Parameter", "Value (:70)", "Value (:71)")) 
3945          print("%-20s %20.15g %20.15g" % ("R2A (500 MHz)", spin70.r2a[r20_key1], spin71.r2a[r20_key1])) 
3946          print("%-20s %20.15g %20.15g" % ("R2B (500 MHz)", spin70.r2b[r20_key1], spin71.r2b[r20_key1])) 
3947          print("%-20s %20.15g %20.15g" % ("R2A (800 MHz)", spin70.r2a[r20_key2], spin71.r2a[r20_key2])) 
3948          print("%-20s %20.15g %20.15g" % ("R2B (800 MHz)", spin70.r2b[r20_key2], spin71.r2b[r20_key2])) 
3949          print("%-20s %20.15g %20.15g" % ("pA", spin70.pA, spin71.pA)) 
3950          print("%-20s %20.15g %20.15g" % ("dw", spin70.dw, spin71.dw)) 
3951          print("%-20s %20.15g %20.15g" % ("kex", spin70.kex, spin71.kex)) 
3952          print("%-20s %20.15g %20.15g\n" % ("chi2", spin70.chi2, spin71.chi2)) 
3953   
3954          # Checks for residue :70. 
3955          self.assertAlmostEqual(spin70.r2a[r20_key1], 6.87485258365614, 4) 
3956          self.assertAlmostEqual(spin70.r2b[r20_key1], 1.26075839074614, 4) 
3957          self.assertAlmostEqual(spin70.r2a[r20_key2], 8.79580446260797, 4) 
3958          self.assertAlmostEqual(spin70.r2b[r20_key2], 51.188411562843, 4) 
3959          self.assertAlmostEqual(spin70.pA, 0.989384178573802, 4) 
3960          self.assertAlmostEqual(spin70.dw, 5.54738203723682, 4) 
3961          self.assertAlmostEqual(spin70.kex/1000, 1831.4566463179/1000, 4) 
3962          self.assertAlmostEqual(spin70.chi2, 50.450410782403, 4) 
3963   
3964          # Checks for residue :71. 
3965          self.assertAlmostEqual(spin71.r2a[r20_key1], 5.04185695754972, 4) 
3966          self.assertAlmostEqual(spin71.r2b[r20_key1], 1.62857899941921, 4) 
3967          self.assertAlmostEqual(spin71.pA, 0.988832866751676, 4) 
3968          self.assertAlmostEqual(spin71.dw, 2.24905251856265, 4) 
3969          self.assertAlmostEqual(spin71.kex/1000, 2397.64122642946/1000, 4) 
3970          self.assertAlmostEqual(spin71.chi2, 15.8586492923672, 4) 
3971   
3972          # Test the conversion to k_AB from kex and pA. 
3973          self.assertEqual(spin70.k_AB, spin70.kex * (1.0 - spin70.pA)) 
3974          self.assertEqual(spin71.k_AB, spin71.kex * (1.0 - spin71.pA)) 
3975   
3976          # Test the conversion to k_BA from kex and pA. 
3977          self.assertEqual(spin70.k_BA, spin70.kex * spin70.pA) 
3978          self.assertEqual(spin71.k_BA, spin71.kex * spin71.pA) 
3979   
3980   
3981 -    def test_hansen_cpmg_data_to_it99(self): 
3982          """Optimisation of Dr. Flemming Hansen's CPMG data to the IT99 dispersion model. 
3983   
3984          This uses the data from Dr. Flemming Hansen's paper at http://dx.doi.org/10.1021/jp074793o.  This is CPMG data with a fixed relaxation time period. 
3985          """ 
3986   
3987          # Base data setup. 
3988          self.setup_hansen_cpmg_data(model='IT99') 
3989   
3990          # Alias the spins. 
3991          spin70 = return_spin(":70") 
3992          spin71 = return_spin(":71") 
3993   
3994          # The R20 keys. 
3995          r20_key1 = generate_r20_key(exp_type=EXP_TYPE_CPMG_SQ, frq=500e6) 
3996          r20_key2 = generate_r20_key(exp_type=EXP_TYPE_CPMG_SQ, frq=800e6) 
3997   
3998          # Set the initial parameter values. 
3999          spin70.r2 = {r20_key1: 8.8, r20_key2: 16.6} 
4000          spin70.dw = 10.0 
4001          spin70.pA = 0.5 
4002          spin70.tex = 1000.09 
4003          spin71.r2 = {r20_key1: 1.0, r20_key2: 1.0} 
4004          spin71.dw = 10.0 
4005          spin71.pA = 0.95 
4006          spin71.tex = 0.1 
4007   
4008          # Low precision optimisation. 
4009          self.interpreter.minimise.execute(min_algor='simplex', line_search=None, hessian_mod=None, hessian_type=None, func_tol=1e-10, grad_tol=None, max_iter=10000, constraints=True, scaling=True, verbosity=1) 
4010   
4011          # Printout. 
4012          print("\n\nOptimised parameters:\n") 
4013          print("%-20s %-20s %-20s" % ("Parameter", "Value (:70)", "Value (:71)")) 
4014          print("%-20s %20.15g %20.15g" % ("R2 (500 MHz)", spin70.r2[r20_key1], spin71.r2[r20_key1])) 
4015          print("%-20s %20.15g %20.15g" % ("R2 (800 MHz)", spin70.r2[r20_key2], spin71.r2[r20_key2])) 
4016          print("%-20s %20.15g %20.15g" % ("dw", spin70.dw, spin71.dw)) 
4017          print("%-20s %20.15g %20.15g" % ("pA", spin70.pA, spin71.pA)) 
4018          print("%-20s %20.15g %20.15g" % ("tex", spin70.tex, spin71.tex)) 
4019          print("%-20s %20.15g %20.15g\n" % ("chi2", spin70.chi2, spin71.chi2)) 
4020   
4021          # Checks for residue :70. 
4022          self.assertAlmostEqual(spin70.r2[r20_key1], 7.24471197811838, 4) 
4023          self.assertAlmostEqual(spin70.r2[r20_key2], 10.0571040704729, 4) 
4024          self.assertAlmostEqual(spin70.dw, 5.2116923222744, 4) 
4025          self.assertAlmostEqual(spin70.pA, 0.990253627907212, 4) 
4026          self.assertAlmostEqual(spin70.tex*1000, 0.000638394793480444*1000, 4) 
4027          self.assertAlmostEqual(spin70.chi2, 93.5135798618747, 4) 
4028   
4029          # Checks for residue :71. 
4030          self.assertAlmostEqual(spin71.r2[r20_key1], 5.05971235970214, 4) 
4031          self.assertAlmostEqual(spin71.r2[r20_key2], 6.96641194493447, 4) 
4032          self.assertAlmostEqual(spin71.dw, 0.435389946897141, 4) 
4033          self.assertAlmostEqual(spin71.pA, 0.500000000213519, 3) 
4034          self.assertAlmostEqual(spin71.tex*1000, 0.000372436400585538*1000, 4) 
4035          self.assertAlmostEqual(spin71.chi2, 23.7895798801404, 4) 
4036   
4037   
4038 -    def test_hansen_cpmg_data_to_lm63(self): 
4039          """Optimisation of Dr. Flemming Hansen's CPMG data to the LM63 dispersion model. 
4040   
4041          This uses the data from Dr. Flemming Hansen's paper at http://dx.doi.org/10.1021/jp074793o.  This is CPMG data with a fixed relaxation time period. 
4042          """ 
4043   
4044          # Base data setup. 
4045          self.setup_hansen_cpmg_data(model='LM63') 
4046   
4047          # Alias the spins. 
4048          spin70 = return_spin(":70") 
4049          spin71 = return_spin(":71") 
4050   
4051          # The R20 keys. 
4052          r20_key1 = generate_r20_key(exp_type=EXP_TYPE_CPMG_SQ, frq=500e6) 
4053          r20_key2 = generate_r20_key(exp_type=EXP_TYPE_CPMG_SQ, frq=800e6) 
4054   
4055          # Set the initial parameter values. 
4056          spin70.r2 = {r20_key1: 7.0, r20_key2: 7.0} 
4057          spin70.phi_ex = 0.3 
4058          spin70.kex = 5000.0 
4059          spin71.r2 = {r20_key1: 5.0, r20_key2: 9.0} 
4060          spin71.phi_ex = 0.1 
4061          spin71.kex = 2500.0 
4062   
4063          # Low precision optimisation. 
4064          self.interpreter.minimise.execute(min_algor='simplex', line_search=None, hessian_mod=None, hessian_type=None, func_tol=1e-25, grad_tol=None, max_iter=10000000, constraints=True, scaling=True, verbosity=1) 
4065   
4066          # Printout. 
4067          print("\n\nOptimised parameters:\n") 
4068          print("%-20s %-20s %-20s" % ("Parameter", "Value (:70)", "Value (:71)")) 
4069          print("%-20s %20.15g %20.15g" % ("R2 (500 MHz)", spin70.r2[r20_key1], spin71.r2[r20_key1])) 
4070          print("%-20s %20.15g %20.15g" % ("R2 (800 MHz)", spin70.r2[r20_key2], spin71.r2[r20_key2])) 
4071          print("%-20s %20.15g %20.15g" % ("phi_ex", spin70.phi_ex, spin71.phi_ex)) 
4072          print("%-20s %20.15g %20.15g" % ("kex", spin70.kex, spin71.kex)) 
4073          print("%-20s %20.15g %20.15g\n" % ("chi2", spin70.chi2, spin71.chi2)) 
4074   
4075          # Checks for residue :70. 
4076          self.assertAlmostEqual(spin70.r2[r20_key1], 6.74362294539099) 
4077          self.assertAlmostEqual(spin70.r2[r20_key2], 6.57406797067481, 6) 
4078          self.assertAlmostEqual(spin70.phi_ex, 0.312733013751449) 
4079          self.assertAlmostEqual(spin70.kex/1000, 4723.09897146338/1000, 6) 
4080          self.assertAlmostEqual(spin70.chi2, 363.534044873483) 
4081   
4082          # Checks for residue :71. 
4083          self.assertAlmostEqual(spin71.r2[r20_key1], 5.00776657729728, 5) 
4084          self.assertAlmostEqual(spin71.phi_ex, 0.0553787825650613, 5) 
4085          self.assertAlmostEqual(spin71.kex/1000, 2781.72292994154/1000, 5) 
4086          self.assertAlmostEqual(spin71.chi2, 17.0776399916287, 5) 
4087   
4088   
4089 -    def test_hansen_cpmg_data_to_lm63_3site(self): 
4090          """Optimisation of Dr. Flemming Hansen's CPMG data to the LM63 dispersion model. 
4091   
4092          This uses the data from Dr. Flemming Hansen's paper at http://dx.doi.org/10.1021/jp074793o.  This is CPMG data with a fixed relaxation time period. 
4093          """ 
4094   
4095          # Base data setup. 
4096          self.setup_hansen_cpmg_data(model='LM63 3-site') 
4097   
4098          # Alias the spins. 
4099          spin70 = return_spin(":70") 
4100          spin71 = return_spin(":71") 
4101   
4102          # The R20 keys. 
4103          r20_key1 = generate_r20_key(exp_type=EXP_TYPE_CPMG_SQ, frq=500e6) 
4104          r20_key2 = generate_r20_key(exp_type=EXP_TYPE_CPMG_SQ, frq=800e6) 
4105   
4106          ## Set the initial parameter values. 
4107          spin70.r2 = {r20_key1: 7.570370921220954, r20_key2: 8.694446951909107} 
4108          spin70.phi_ex_B = 0.14872003058250227 
4109          spin70.phi_ex_C = 0.1319419923472704 
4110          spin70.kB = 4103.672910444741 
4111          spin70.kC = 7029.001690726248 
4112          spin71.r2 = {r20_key1: 5.1347793381636, r20_key2: 7.156573986051575} 
4113          spin71.phi_ex_B = 0.04013553485505605 
4114          spin71.phi_ex_C = 0.020050748406928887 
4115          spin71.kB = 4045.3007136121364 
4116          spin71.kC = 3586.38798270774 
4117   
4118          #self.interpreter.relax_disp.r20_from_min_r2eff(force=False) 
4119          #self.interpreter.minimise.grid_search(lower=None, upper=None, inc=41, constraints=True, verbosity=1) 
4120   
4121          # Low precision optimisation. 
4122          self.interpreter.minimise.execute(min_algor='simplex', line_search=None, hessian_mod=None, hessian_type=None, func_tol=1e-25, grad_tol=None, max_iter=10000000, constraints=True, scaling=True, verbosity=1) 
4123   
4124          # Printout. 
4125          print("\n\nOptimised parameters:\n") 
4126          print("%-20s %-20s %-20s" % ("Parameter", "Value (:70)", "Value (:71)")) 
4127          print("%-20s %20.15g %20.15g" % ("R2 (500 MHz)", spin70.r2[r20_key1], spin71.r2[r20_key1])) 
4128          print("%-20s %20.15g %20.15g" % ("R2 (800 MHz)", spin70.r2[r20_key2], spin71.r2[r20_key2])) 
4129          print("%-20s %20.15g %20.15g" % ("phi_ex_B", spin70.phi_ex_B, spin71.phi_ex_B)) 
4130          print("%-20s %20.15g %20.15g" % ("phi_ex_C", spin70.phi_ex_C, spin71.phi_ex_C)) 
4131          print("%-20s %20.15g %20.15g" % ("kB", spin70.kB, spin71.kB)) 
4132          print("%-20s %20.15g %20.15g" % ("kC", spin70.kC, spin71.kC)) 
4133          print("%-20s %20.15g %20.15g\n" % ("chi2", spin70.chi2, spin71.chi2)) 
4134   
4135          # Checks for residue :70. 
4136          self.assertAlmostEqual(spin70.r2[r20_key1], 6.7436230253685, 5) 
4137          self.assertAlmostEqual(spin70.r2[r20_key2], 6.57406813008828, 6) 
4138          self.assertAlmostEqual(spin70.phi_ex_B, 0.206304023079778, 5) 
4139          self.assertAlmostEqual(spin70.phi_ex_C, 0.106428983339627, 5) 
4140          self.assertAlmostEqual(spin70.kB/1000, 4723.09897652589/1000, 6) 
4141          self.assertAlmostEqual(spin70.kC/1000, 4723.09876196409/1000, 6) 
4142          self.assertAlmostEqual(spin70.chi2, 363.534044873483, 5) 
4143   
4144          # Checks for residue :71. 
4145          self.assertAlmostEqual(spin71.r2[r20_key1], 4.96612095596752, 5) 
4146          self.assertAlmostEqual(spin71.phi_ex_B, 0.00398262266512895, 5) 
4147          self.assertAlmostEqual(spin71.phi_ex_C, 0.0555791581291262, 5) 
4148          self.assertAlmostEqual(spin71.kB/1000, 1323.33195689832/1000, 5) 
4149          self.assertAlmostEqual(spin71.kC/1000, 3149.58971568059/1000, 5) 
4150          self.assertAlmostEqual(spin71.chi2, 16.2620934464368) 
4151   
4152   
4153 -    def test_hansen_cpmg_data_to_ns_cpmg_2site_3D(self): 
4154          """Optimisation of Dr. Flemming Hansen's CPMG data to the 'NS CPMG 2-site 3D' dispersion model. 
4155   
4156          This uses the data from Dr. Flemming Hansen's paper at http://dx.doi.org/10.1021/jp074793o.  This is CPMG data with a fixed relaxation time period. 
4157          """ 
4158   
4159          # Base data setup. 
4160          self.setup_hansen_cpmg_data(model='NS CPMG 2-site 3D') 
4161   
4162          # Alias the spins. 
4163          spin70 = return_spin(":70") 
4164          spin71 = return_spin(":71") 
4165   
4166          # The R20 keys. 
4167          r20_key1 = generate_r20_key(exp_type=EXP_TYPE_CPMG_SQ, frq=500e6) 
4168          r20_key2 = generate_r20_key(exp_type=EXP_TYPE_CPMG_SQ, frq=800e6) 
4169   
4170          # Set the initial parameter values. 
4171          spin70.r2 = {r20_key1: 6.994165925, r20_key2: 9.428129427} 
4172          spin70.pA = 0.9897754407 
4173          spin70.dw = 5.642418428 
4174          spin70.kex = 1743.666375 
4175          spin71.r2 = {r20_key1: 4.978654237, r20_key2: 9.276918959} 
4176          spin71.pA = 0.9968032899 
4177          spin71.dw = 4.577891393 
4178          spin71.kex = 1830.044597 
4179   
4180          # Low precision optimisation. 
4181          self.interpreter.minimise.execute(min_algor='simplex', line_search=None, hessian_mod=None, hessian_type=None, func_tol=1e-05, grad_tol=None, max_iter=1000, constraints=False, scaling=True, verbosity=1) 
4182   
4183          # Printout. 
4184          print("\n\nOptimised parameters:\n") 
4185          print("%-20s %-20s %-20s" % ("Parameter", "Value (:70)", "Value (:71)")) 
4186          print("%-20s %20.15g %20.15g" % ("R2 (500 MHz)", spin70.r2[r20_key1], spin71.r2[r20_key1])) 
4187          print("%-20s %20.15g %20.15g" % ("R2 (800 MHz)", spin70.r2[r20_key2], spin71.r2[r20_key2])) 
4188          print("%-20s %20.15g %20.15g" % ("pA", spin70.pA, spin71.pA)) 
4189          print("%-20s %20.15g %20.15g" % ("dw", spin70.dw, spin71.dw)) 
4190          print("%-20s %20.15g %20.15g" % ("kex", spin70.kex, spin71.kex)) 
4191          print("%-20s %20.15g %20.15g\n" % ("chi2", spin70.chi2, spin71.chi2)) 
4192   
4193          # Checks for residue :70. 
4194          self.assertAlmostEqual(spin70.r2[r20_key1], 6.95797760459016, 4) 
4195          self.assertAlmostEqual(spin70.r2[r20_key2], 9.39628959312699, 4) 
4196          self.assertAlmostEqual(spin70.pA, 0.989700985380975, 4) 
4197          self.assertAlmostEqual(spin70.dw, 5.6733714171086, 4) 
4198          self.assertAlmostEqual(spin70.kex/1000, 1713.63101361545/1000, 4) 
4199          self.assertAlmostEqual(spin70.chi2, 52.5106928523775, 4) 
4200   
4201          # Checks for residue :71. 
4202          self.assertAlmostEqual(spin71.r2[r20_key1], 4.99893565849977, 4) 
4203          self.assertAlmostEqual(spin71.r2[r20_key2], 6.89825625944034, 4) 
4204          self.assertAlmostEqual(spin71.pA, 0.986716058519642, 4) 
4205          self.assertAlmostEqual(spin71.dw, 2.09292495350993, 4) 
4206          self.assertAlmostEqual(spin71.kex/1000, 2438.04423541463/1000, 4) 
4207          self.assertAlmostEqual(spin71.chi2, 15.164490242352, 4) 
4208   
4209          # Test the conversion to k_AB from kex and pA. 
4210          self.assertEqual(spin70.k_AB, spin70.kex * (1.0 - spin70.pA)) 
4211          self.assertEqual(spin71.k_AB, spin71.kex * (1.0 - spin71.pA)) 
4212   
4213          # Test the conversion to k_BA from kex and pA. 
4214          self.assertEqual(spin70.k_BA, spin70.kex * spin70.pA) 
4215          self.assertEqual(spin71.k_BA, spin71.kex * spin71.pA) 
4216   
4217   
4218 -    def test_hansen_cpmg_data_to_ns_cpmg_2site_3D_full(self): 
4219          """Optimisation of Dr. Flemming Hansen's CPMG data to the 'NS CPMG 2-site 3D full' dispersion model. 
4220   
4221          This uses the data from Dr. Flemming Hansen's paper at http://dx.doi.org/10.1021/jp074793o.  This is CPMG data with a fixed relaxation time period. 
4222          """ 
4223   
4224          # Base data setup. 
4225          self.setup_hansen_cpmg_data(model='NS CPMG 2-site 3D full') 
4226   
4227          # Alias the spins. 
4228          spin70 = return_spin(":70") 
4229          spin71 = return_spin(":71") 
4230   
4231          # The R20 keys. 
4232          r20_key1 = generate_r20_key(exp_type=EXP_TYPE_CPMG_SQ, frq=500e6) 
4233          r20_key2 = generate_r20_key(exp_type=EXP_TYPE_CPMG_SQ, frq=800e6) 
4234   
4235          # Set the initial parameter values. 
4236          spin70.r2a = {r20_key1: 6.644753428, r20_key2: 7.891776687} 
4237          spin70.r2b = {r20_key1: 7.163478485, r20_key2: 138.5170395} 
4238          spin70.pA = 0.9884781357 
4239          spin70.dw = 5.456507396 
4240          spin70.kex = 1906.521189 
4241          spin71.r2a = {r20_key1: 4.99893524108981, r20_key2: 100.0} 
4242          spin71.r2b = {r20_key1: 8.27456243639973, r20_key2: 100.0} 
4243          spin71.pA = 0.986709616684097 
4244          spin71.dw = 2.09245158280905 
4245          spin71.kex = 2438.2766211401 
4246   
4247          # Low precision optimisation. 
4248          self.interpreter.minimise.execute(min_algor='simplex', line_search=None, hessian_mod=None, hessian_type=None, func_tol=1e-05, grad_tol=None, max_iter=1000, constraints=False, scaling=True, verbosity=1) 
4249   
4250          # Printout. 
4251          print("\n\nOptimised parameters:\n") 
4252          print("%-20s %-20s %-20s" % ("Parameter", "Value (:70)", "Value (:71)")) 
4253          print("%-20s %20.15g %20.15g" % ("R2A (500 MHz)", spin70.r2a[r20_key1], spin71.r2a[r20_key1])) 
4254          print("%-20s %20.15g %20.15g" % ("R2B (500 MHz)", spin70.r2b[r20_key1], spin71.r2b[r20_key1])) 
4255          print("%-20s %20.15g %20.15g" % ("R2A (800 MHz)", spin70.r2a[r20_key2], spin71.r2a[r20_key2])) 
4256          print("%-20s %20.15g %20.15g" % ("R2B (800 MHz)", spin70.r2b[r20_key2], spin71.r2b[r20_key2])) 
4257          print("%-20s %20.15g %20.15g" % ("pA", spin70.pA, spin71.pA)) 
4258          print("%-20s %20.15g %20.15g" % ("dw", spin70.dw, spin71.dw)) 
4259          print("%-20s %20.15g %20.15g" % ("kex", spin70.kex, spin71.kex)) 
4260          print("%-20s %20.15g %20.15g\n" % ("chi2", spin70.chi2, spin71.chi2)) 
4261   
4262          # Checks for residue :70. 
4263          self.assertAlmostEqual(spin70.r2a[r20_key1], 6.61176004043484, 4) 
4264          self.assertAlmostEqual(spin70.r2b[r20_key1], 7.4869316381241, 4) 
4265          self.assertAlmostEqual(spin70.r2a[r20_key2], 7.78200386067591, 4) 
4266          self.assertAlmostEqual(spin70.r2b[r20_key2], 141.703593742468, 4) 
4267          self.assertAlmostEqual(spin70.pA, 0.988404987055969, 4) 
4268          self.assertAlmostEqual(spin70.dw, 5.4497360203213, 4) 
4269          self.assertAlmostEqual(spin70.kex/1000, 1934.09304607082/1000, 4) 
4270          self.assertAlmostEqual(spin70.chi2, 44.6793752187925, 4) 
4271   
4272          # Checks for residue :71. 
4273          self.assertAlmostEqual(spin71.r2a[r20_key1], 4.6013095731966, 4) 
4274          self.assertAlmostEqual(spin71.r2b[r20_key1], 13.3245678276332, 4) 
4275          self.assertAlmostEqual(spin71.r2a[r20_key2], 2.08243621257779, 4) 
4276          self.assertAlmostEqual(spin71.r2b[r20_key2], 153.355765094575, 4) 
4277          self.assertAlmostEqual(spin71.pA, 0.9665748685124, 4) 
4278          self.assertAlmostEqual(spin71.dw, 1.41898001408953, 4) 
4279          self.assertAlmostEqual(spin71.kex/1000, 2580.65795560688/1000, 4) 
4280          self.assertAlmostEqual(spin71.chi2, 13.4937006732165, 4) 
4281   
4282          # Test the conversion to k_AB from kex and pA. 
4283          self.assertEqual(spin70.k_AB, spin70.kex * (1.0 - spin70.pA)) 
4284          self.assertEqual(spin71.k_AB, spin71.kex * (1.0 - spin71.pA)) 
4285   
4286          # Test the conversion to k_BA from kex and pA. 
4287          self.assertEqual(spin70.k_BA, spin70.kex * spin70.pA) 
4288          self.assertEqual(spin71.k_BA, spin71.kex * spin71.pA) 
4289   
4290   
4291 -    def test_hansen_cpmg_data_to_ns_cpmg_2site_expanded(self): 
4292          """Optimisation of Dr. Flemming Hansen's CPMG data to the 'NS CPMG 2-site expanded' dispersion model. 
4293   
4294          This uses the data from Dr. Flemming Hansen's paper at http://dx.doi.org/10.1021/jp074793o.  This is CPMG data with a fixed relaxation time period. 
4295          """ 
4296   
4297          # Base data setup. 
4298          self.setup_hansen_cpmg_data(model='NS CPMG 2-site expanded') 
4299   
4300          # Alias the spins. 
4301          spin70 = return_spin(":70") 
4302          spin71 = return_spin(":71") 
4303   
4304          # The R20 keys. 
4305          r20_key1 = generate_r20_key(exp_type=EXP_TYPE_CPMG_SQ, frq=500e6) 
4306          r20_key2 = generate_r20_key(exp_type=EXP_TYPE_CPMG_SQ, frq=800e6) 
4307   
4308          # Set the initial parameter values. 
4309          spin70.r2 = {r20_key1: 7.0, r20_key2: 9.0} 
4310          spin70.pA = 0.9 
4311          spin70.dw = 6.0 
4312          spin70.kex = 1500.0 
4313          spin71.r2 = {r20_key1: 5.0, r20_key2: 9.0} 
4314          spin71.pA = 0.9 
4315          spin71.dw = 4.0 
4316          spin71.kex = 1900.0 
4317   
4318          # Low precision optimisation. 
4319          self.interpreter.minimise.execute(min_algor='simplex', line_search=None, hessian_mod=None, hessian_type=None, func_tol=1e-05, grad_tol=None, max_iter=1000, constraints=True, scaling=True, verbosity=1) 
4320   
4321          # Printout. 
4322          print("\n\nOptimised parameters:\n") 
4323          print("%-20s %-20s %-20s" % ("Parameter", "Value (:70)", "Value (:71)")) 
4324          print("%-20s %20.15g %20.15g" % ("R2 (500 MHz)", spin70.r2[r20_key1], spin71.r2[r20_key1])) 
4325          print("%-20s %20.15g %20.15g" % ("R2 (800 MHz)", spin70.r2[r20_key2], spin71.r2[r20_key2])) 
4326          print("%-20s %20.15g %20.15g" % ("pA", spin70.pA, spin71.pA)) 
4327          print("%-20s %20.15g %20.15g" % ("dw", spin70.dw, spin71.dw)) 
4328          print("%-20s %20.15g %20.15g" % ("kex", spin70.kex, spin71.kex)) 
4329          print("%-20s %20.15g %20.15g\n" % ("chi2", spin70.chi2, spin71.chi2)) 
4330   
4331          # Checks for residue :70. 
4332          self.assertAlmostEqual(spin70.r2[r20_key1], 6.95813330991529, 4) 
4333          self.assertAlmostEqual(spin70.r2[r20_key2], 9.39663480561524, 4) 
4334          self.assertAlmostEqual(spin70.pA, 0.989700843879574, 4) 
4335          self.assertAlmostEqual(spin70.dw, 5.67315878825691, 4) 
4336          self.assertAlmostEqual(spin70.kex/1000, 1713.56110716632/1000, 4) 
4337          self.assertAlmostEqual(spin70.chi2, 52.5106879242812, 4) 
4338   
4339          # Checks for residue :71. 
4340          self.assertAlmostEqual(spin71.r2[r20_key1], 4.99881666793312, 4) 
4341          self.assertAlmostEqual(spin71.r2[r20_key2], 6.89817482453042, 4) 
4342          self.assertAlmostEqual(spin71.pA, 0.986712911453639, 4) 
4343          self.assertAlmostEqual(spin71.dw, 2.09273069372236, 4) 
4344          self.assertAlmostEqual(spin71.kex/1000, 2438.20525930405/1000, 4) 
4345          self.assertAlmostEqual(spin71.chi2, 15.1644913030633, 4) 
4346   
4347          # Test the conversion to k_AB from kex and pA. 
4348          self.assertEqual(spin70.k_AB, spin70.kex * (1.0 - spin70.pA)) 
4349          self.assertEqual(spin71.k_AB, spin71.kex * (1.0 - spin71.pA)) 
4350   
4351          # Test the conversion to k_BA from kex and pA. 
4352          self.assertEqual(spin70.k_BA, spin70.kex * spin70.pA) 
4353          self.assertEqual(spin71.k_BA, spin71.kex * spin71.pA) 
4354   
4355   
4356 -    def test_hansen_cpmg_data_to_ns_cpmg_2site_star(self): 
4357          """Optimisation of Dr. Flemming Hansen's CPMG data to the 'NS CPMG 2-site star' dispersion model. 
4358   
4359          This uses the data from Dr. Flemming Hansen's paper at http://dx.doi.org/10.1021/jp074793o.  This is CPMG data with a fixed relaxation time period. 
4360          """ 
4361   
4362          # Base data setup. 
4363          self.setup_hansen_cpmg_data(model='NS CPMG 2-site star') 
4364   
4365          # Alias the spins. 
4366          spin70 = return_spin(":70") 
4367          spin71 = return_spin(":71") 
4368   
4369          # The R20 keys. 
4370          r20_key1 = generate_r20_key(exp_type=EXP_TYPE_CPMG_SQ, frq=500e6) 
4371          r20_key2 = generate_r20_key(exp_type=EXP_TYPE_CPMG_SQ, frq=800e6) 
4372   
4373          # Set the initial parameter values. 
4374          spin70.r2 = {r20_key1: 6.996327746, r20_key2: 9.452051268} 
4375          spin70.pA = 0.9897519798 
4376          spin70.dw = 5.644862195 
4377          spin70.kex = 1723.820567 
4378          spin71.r2 = {r20_key1: 4.978654237, r20_key2: 9.276918959} 
4379          spin71.pA = 0.9968032899 
4380          spin71.dw = 4.577891393 
4381          spin71.kex = 1830.044597 
4382   
4383          # Low precision optimisation. 
4384          self.interpreter.minimise.execute(min_algor='simplex', line_search=None, hessian_mod=None, hessian_type=None, func_tol=1e-05, grad_tol=None, max_iter=1000, constraints=False, scaling=True, verbosity=1) 
4385   
4386          # Printout. 
4387          print("\n\nOptimised parameters:\n") 
4388          print("%-20s %-20s %-20s" % ("Parameter", "Value (:70)", "Value (:71)")) 
4389          print("%-20s %20.15g %20.15g" % ("R2 (500 MHz)", spin70.r2[r20_key1], spin71.r2[r20_key1])) 
4390          print("%-20s %20.15g %20.15g" % ("R2 (800 MHz)", spin70.r2[r20_key2], spin71.r2[r20_key2])) 
4391          print("%-20s %20.15g %20.15g" % ("pA", spin70.pA, spin71.pA)) 
4392          print("%-20s %20.15g %20.15g" % ("dw", spin70.dw, spin71.dw)) 
4393          print("%-20s %20.15g %20.15g" % ("kex", spin70.kex, spin71.kex)) 
4394          print("%-20s %20.15g %20.15g\n" % ("chi2", spin70.chi2, spin71.chi2)) 
4395   
4396          # Checks for residue :70. 
4397          self.assertAlmostEqual(spin70.r2[r20_key1], 6.95543947938561, 1) 
4398          self.assertAlmostEqual(spin70.r2[r20_key2], 9.38991914134929, 1) 
4399          self.assertAlmostEqual(spin70.pA, 0.989702750971153, 3) 
4400          self.assertAlmostEqual(spin70.dw, 5.67527122494516, 1) 
4401          self.assertAlmostEqual(spin70.kex/1000, 1715.72032391817/1000, 1) 
4402          self.assertAlmostEqual(spin70.chi2, 52.5011991483842, 1) 
4403   
4404          # Checks for residue :71. 
4405          self.assertAlmostEqual(spin71.r2[r20_key1], 4.992594256544, 1) 
4406          self.assertAlmostEqual(spin71.pA, 0.986716058519642, 2) 
4407          self.assertAlmostEqual(spin71.dw/100, 2.09292495350993/100, 2) 
4408          self.assertAlmostEqual(spin71.kex/100000, 2438.04423541463/100000, 2) 
4409          self.assertAlmostEqual(spin71.chi2/100, 15.1644902423334/100, 1) 
4410   
4411          # Test the conversion to k_AB from kex and pA. 
4412          self.assertEqual(spin70.k_AB, spin70.kex * (1.0 - spin70.pA)) 
4413          self.assertEqual(spin71.k_AB, spin71.kex * (1.0 - spin71.pA)) 
4414   
4415          # Test the conversion to k_BA from kex and pA. 
4416          self.assertEqual(spin70.k_BA, spin70.kex * spin70.pA) 
4417          self.assertEqual(spin71.k_BA, spin71.kex * spin71.pA) 
4418   
4419   
4420 -    def test_hansen_cpmg_data_to_ns_cpmg_2site_star_full(self): 
4421          """Optimisation of Dr. Flemming Hansen's CPMG data to the 'NS CPMG 2-site star full' dispersion model. 
4422   
4423          This uses the data from Dr. Flemming Hansen's paper at http://dx.doi.org/10.1021/jp074793o.  This is CPMG data with a fixed relaxation time period. 
4424          """ 
4425   
4426          # Base data setup. 
4427          self.setup_hansen_cpmg_data(model='NS CPMG 2-site star full') 
4428   
4429          # Alias the spins. 
4430          spin70 = return_spin(":70") 
4431          spin71 = return_spin(":71") 
4432   
4433          # The R20 keys. 
4434          r20_key1 = generate_r20_key(exp_type=EXP_TYPE_CPMG_SQ, frq=500e6) 
4435          r20_key2 = generate_r20_key(exp_type=EXP_TYPE_CPMG_SQ, frq=800e6) 
4436   
4437          # Set the initial parameter values. 
4438          spin70.r2a = {r20_key1: 6.44836878645126, r20_key2: 7.00382877393494} 
4439          spin70.r2b = {r20_key1: 12.2083127421994, r20_key2: 199.862962628402} 
4440          spin70.pA = 0.987648082613451 
4441          spin70.dw = 5.30679853807572 
4442          spin70.kex = 2033.25380420666 
4443          spin71.r2a = {r20_key1: 4.992594256544, r20_key2: 6.98674718938435} 
4444          spin71.r2b = {r20_key1: 4.992594256544, r20_key2: 6.98674718938435} 
4445          spin71.pA = 0.992258541625787 
4446          spin71.dw = 2.75140650899058 
4447          spin71.kex = 2106.60885247431 
4448   
4449          # Low precision optimisation. 
4450          self.interpreter.minimise.calculate() 
4451   
4452          # Checks for residue :70. 
4453          self.assertAlmostEqual(spin70.chi2/10, 45.773987568491123/10, 2) 
4454          self.assertAlmostEqual(spin71.chi2/10, 17.329385665659192/10, 2) 
4455   
4456   
4457 -    def test_hansen_cpmgfit_input(self): 
4458          """Conversion of Dr. Flemming Hansen's CPMG R2eff values into input files for CPMGFit. 
4459   
4460          This uses the data from Dr. Flemming Hansen's paper at http://dx.doi.org/10.1021/jp074793o.  This is CPMG data with a fixed relaxation time period. 
4461          """ 
4462   
4463          # Load the R2eff results file. 
4464          file_name = status.install_path + sep+'test_suite'+sep+'shared_data'+sep+'dispersion'+sep+'Hansen'+sep+'r2eff_pipe' 
4465          self.interpreter.results.read(file_name) 
4466          self.interpreter.deselect.spin(':4') 
4467   
4468          # Set up the model. 
4469          self.interpreter.relax_disp.select_model('LM63') 
4470   
4471          # Generate the input files. 
4472          self.interpreter.relax_disp.cpmgfit_input(force=True, dir=ds.tmpdir) 
4473   
4474          # What the files should contain. 
4475          batch_file = ['#! /bin/sh\n', '\n', 'cpmgfit -grid -xmgr -f spin_70_N.in | tee spin_70_N.out\n', 'cpmgfit -grid -xmgr -f spin_71_N.in | tee spin_71_N.out\n'] 
4476          spin1 = [ 
4477              "title :70@N\n", 
4478              "fields 2 11.7432964915 18.7892743865\n", 
4479              "function CPMG\n", 
4480              "R2 1 10 20\n", 
4481              "Rex 0 100.0 100\n", 
4482              "Tau 0 10.0 100\n", 
4483              "xmgr\n", 
4484              "@ xaxis label \"1/tcp (1/ms)\"\n", 
4485              "@ yaxis label \"R2(tcp) (rad/s)\"\n", 
4486              "@ xaxis ticklabel format decimal\n", 
4487              "@ yaxis ticklabel format decimal\n", 
4488              "@ xaxis ticklabel char size 0.8\n", 
4489              "@ yaxis ticklabel char size 0.8\n", 
4490              "@ world xmin 0.0\n", 
4491              "data\n", 
4492              "0.133333             16.045541            0.310925             11.743296           \n", 
4493              "0.266667             14.877925            0.303217             11.743296           \n", 
4494              "0.400000             14.357820            0.299894             11.743296           \n", 
4495              "0.533333             12.664495            0.289532             11.743296           \n", 
4496              "0.666667             12.363205            0.287760             11.743296           \n", 
4497              "0.800000             11.092532            0.280514             11.743296           \n", 
4498              "0.933333             10.566090            0.277619             11.743296           \n", 
4499              "1.066667             9.805807             0.273544             11.743296           \n", 
4500              "1.200000             9.564301             0.272276             11.743296           \n", 
4501              "1.333333             9.015634             0.269442             11.743296           \n", 
4502              "1.466667             8.607765             0.267375             11.743296           \n", 
4503              "1.600000             8.279997             0.265740             11.743296           \n", 
4504              "1.733333             8.474536             0.266708             11.743296           \n", 
4505              "1.866667             8.158973             0.265141             11.743296           \n", 
4506              "2.000000             7.988631             0.264304             11.743296           \n", 
4507              "0.133333             22.224914            0.166231             18.789274           \n", 
4508              "0.266667             21.230874            0.162377             18.789274           \n", 
4509              "0.400000             20.603704            0.160017             18.789274           \n", 
4510              "0.533333             20.327797            0.158996             18.789274           \n", 
4511              "0.666667             18.855377            0.153719             18.789274           \n", 
4512              "0.800000             18.537531            0.152617             18.789274           \n", 
4513              "0.933333             17.508069            0.149138             18.789274           \n", 
4514              "1.066667             16.035604            0.144391             18.789274           \n", 
4515              "1.200000             15.168192            0.141717             18.789274           \n", 
4516              "1.333333             14.431802            0.139516             18.789274           \n", 
4517              "1.466667             14.034137            0.138354             18.789274           \n", 
4518              "1.600000             12.920148            0.135192             18.789274           \n", 
4519              "1.733333             12.653673            0.134456             18.789274           \n", 
4520              "1.866667             12.610864            0.134338             18.789274           \n", 
4521              "2.000000             11.969303            0.132601             18.789274           \n" 
4522          ] 
4523          spin2 = [ 
4524              "title :71@N\n", 
4525              "fields 2 11.7432964915 18.7892743865\n", 
4526              "function CPMG\n", 
4527              "R2 1 10 20\n", 
4528              "Rex 0 100.0 100\n", 
4529              "Tau 0 10.0 100\n", 
4530              "xmgr\n", 
4531              "@ xaxis label \"1/tcp (1/ms)\"\n", 
4532              "@ yaxis label \"R2(tcp) (rad/s)\"\n", 
4533              "@ xaxis ticklabel format decimal\n", 
4534              "@ yaxis ticklabel format decimal\n", 
4535              "@ xaxis ticklabel char size 0.8\n", 
4536              "@ yaxis ticklabel char size 0.8\n", 
4537              "@ world xmin 0.0\n", 
4538              "data\n", 
4539              "0.133333             7.044342             0.170035             11.743296           \n", 
4540              "0.266667             6.781033             0.169228             11.743296           \n", 
4541              "0.400000             6.467623             0.168279             11.743296           \n", 
4542              "0.533333             6.333340             0.167876             11.743296           \n", 
4543              "0.666667             6.323238             0.167846             11.743296           \n", 
4544              "0.800000             6.005245             0.166902             11.743296           \n", 
4545              "0.933333             5.767052             0.166203             11.743296           \n", 
4546              "1.066667             5.476968             0.165361             11.743296           \n", 
4547              "1.200000             5.469949             0.165341             11.743296           \n", 
4548              "1.333333             5.295113             0.164838             11.743296           \n", 
4549              "1.466667             5.435648             0.165242             11.743296           \n", 
4550              "1.600000             5.410400             0.165169             11.743296           \n", 
4551              "1.733333             5.437554             0.165247             11.743296           \n", 
4552              "1.866667             5.176844             0.164501             11.743296           \n", 
4553              "2.000000             5.227232             0.164644             11.743296           \n", 
4554              "0.133333             11.530903            0.081928             18.789274           \n", 
4555              "0.266667             10.983094            0.081041             18.789274           \n", 
4556              "0.400000             10.512403            0.080294             18.789274           \n", 
4557              "0.533333             9.984805             0.079473             18.789274           \n", 
4558              "0.666667             9.573163             0.078845             18.789274           \n", 
4559              "0.800000             9.178810             0.078253             18.789274           \n", 
4560              "0.933333             8.935719             0.077893             18.789274           \n", 
4561              "1.066667             8.610147             0.077416             18.789274           \n", 
4562              "1.200000             8.353778             0.077045             18.789274           \n", 
4563              "1.333333             8.173729             0.076787             18.789274           \n", 
4564              "1.466667             8.091607             0.076670             18.789274           \n", 
4565              "1.600000             7.706420             0.076126             18.789274           \n", 
4566              "1.733333             7.709125             0.076129             18.789274           \n", 
4567              "1.866667             7.610856             0.075992             18.789274           \n", 
4568              "2.000000             7.552584             0.075911             18.789274           \n", 
4569          ] 
4570   
4571          # Check the batch file. 
4572          print("\nChecking the batch file.") 
4573          file = open("%s%sbatch_run.sh" % (ds.tmpdir, sep)) 
4574          lines = file.readlines() 
4575          file.close() 
4576          for i in range(len(lines)): 
4577              self.assertEqual(batch_file[i], lines[i]) 
4578   
4579          # Check spin :70@N. 
4580          print("\nChecking the spin :70@N input file.") 
4581          file = open("%s%sspin%s.in" % (ds.tmpdir, sep, '_70_N')) 
4582          lines = file.readlines() 
4583          file.close() 
4584          for i in range(len(spin1)): 
4585              print("%s\"%s\\n\"," % (" "*12, lines[i][:-1])) 
4586          for i in range(len(lines)): 
4587              self.assertEqual(spin1[i], lines[i]) 
4588   
4589          # Check spin :71@N. 
4590          print("\nChecking the spin :71@N input file.") 
4591          file = open("%s%sspin%s.in" % (ds.tmpdir, sep, '_71_N')) 
4592          lines = file.readlines() 
4593          file.close() 
4594          for i in range(len(lines)): 
4595              print("%s\"%s\\n\"," % (" "*12, lines[i][:-1])) 
4596          for i in range(len(spin2)): 
4597              self.assertEqual(spin2[i], lines[i]) 
4598   
4599   
4600 -    def test_korzhnev_2005_15n_dq_data(self): 
4601          """Optimisation of the Korzhnev et al., 2005 15N DQ CPMG data using the 'NS MMQ 2-site' model. 
4602   
4603          This uses the data from Dmitry Korzhnev's paper at U{DOI: 10.1021/ja054550e<http://dx.doi.org/10.1021/ja054550e>}.  This is the 1H SQ, 15N SQ, ZQ, DQ, 1H MQ and 15N MQ data for residue Asp 9 of the Fyn SH3 domain mutant. 
4604   
4605          Here only the 15N DQ data will be optimised.  The values found by cpmg_fit using just this data are: 
4606   
4607              - r2 = {'500': 9.487269007171426, '600': 11.718267257562591, '800': 13.624551743116887}, 
4608              - pA = 0.965402506690231, 
4609              - dw = 0.805197170133360, 
4610              - dwH = -0.595536627771890, 
4611              - kex = 569.003663067619868, 
4612              - chi2 = 9.297671357952812. 
4613          """ 
4614   
4615          # Base data setup. 
4616          self.setup_korzhnev_2005_data(data_list=['DQ']) 
4617   
4618          # Alias the spin. 
4619          spin = return_spin(":9@N") 
4620   
4621          # The R20 keys. 
4622          r20_key1 = generate_r20_key(exp_type=EXP_TYPE_CPMG_DQ, frq=500e6) 
4623          r20_key2 = generate_r20_key(exp_type=EXP_TYPE_CPMG_DQ, frq=600e6) 
4624          r20_key3 = generate_r20_key(exp_type=EXP_TYPE_CPMG_DQ, frq=800e6) 
4625   
4626          # Set the initial parameter values. 
4627          spin.r2 = {r20_key1: 9.48527908326952, r20_key2: 11.7135951595536, r20_key3: 13.6153887849344} 
4628          spin.pA = 0.965638501551899 
4629          spin.dw = 2.8537583461577 
4630          spin.dwH = -0.387633062766635 
4631          spin.kex = 573.704033851592 
4632   
4633          # Low precision optimisation. 
4634          self.interpreter.minimise.execute(min_algor='simplex', func_tol=1e-05, max_iter=1000) 
4635   
4636          # Monte Carlo simulations. 
4637          self.interpreter.monte_carlo.setup(number=2) 
4638          self.interpreter.monte_carlo.create_data(method='back_calc') 
4639          self.interpreter.monte_carlo.initial_values() 
4640          self.interpreter.minimise.execute(min_algor='simplex', max_iter=10) 
4641          self.interpreter.monte_carlo.error_analysis() 
4642   
4643          # Plot the dispersion curves. 
4644          self.interpreter.relax_disp.plot_disp_curves(dir=ds.tmpdir, force=True) 
4645   
4646          # Save the results. 
4647          self.interpreter.state.save('state', dir=ds.tmpdir, compress_type=1, force=True) 
4648   
4649          # Printout. 
4650          print("\n\nOptimised parameters:\n") 
4651          print("%-20s %-20s" % ("Parameter", "Value (:9)")) 
4652          print("%-20s %20.15g" % ("R2 (500 MHz)", spin.r2[r20_key1])) 
4653          print("%-20s %20.15g" % ("R2 (600 MHz)", spin.r2[r20_key2])) 
4654          print("%-20s %20.15g" % ("R2 (800 MHz)", spin.r2[r20_key3])) 
4655          print("%-20s %20.15g" % ("pA", spin.pA)) 
4656          print("%-20s %20.15g" % ("dw", spin.dw)) 
4657          print("%-20s %20.15g" % ("dwH", spin.dwH)) 
4658          print("%-20s %20.15g" % ("kex", spin.kex)) 
4659          print("%-20s %20.15g\n" % ("chi2", spin.chi2)) 
4660   
4661          # Checks for residue :9. 
4662          self.assertAlmostEqual(spin.r2[r20_key1], 9.48527908326952, 2) 
4663          self.assertAlmostEqual(spin.r2[r20_key2], 11.7135951595536, 2) 
4664          self.assertAlmostEqual(spin.r2[r20_key3], 13.6153887849344, 2) 
4665          self.assertAlmostEqual(spin.pA, 0.965638501551899, 4) 
4666          self.assertAlmostEqual(spin.dw, 2.8537583461577, 1) 
4667          self.assertAlmostEqual(spin.dwH, -0.387633062766635, 2) 
4668          self.assertAlmostEqual(spin.kex/1000, 573.704033851592/1000, 3) 
4669          self.assertAlmostEqual(spin.chi2, 9.29563496654824, 2) 
4670   
4671   
4672 -    def test_korzhnev_2005_15n_mq_data(self): 
4673          """Optimisation of the Korzhnev et al., 2005 15N MQ CPMG data using the 'NS MMQ 2-site' model. 
4674   
4675          This uses the data from Dmitry Korzhnev's paper at U{DOI: 10.1021/ja054550e<http://dx.doi.org/10.1021/ja054550e>}.  This is the 1H SQ, 15N SQ, ZQ, DQ, 1H MQ and 15N MQ data for residue Asp 9 of the Fyn SH3 domain mutant. 
4676   
4677          Here only the 15N MQ data will be optimised.  The values found by cpmg_fit using just this data are: 
4678   
4679              - r2 = {'500': 5.993083514798655, '600': 6.622184438384841, '800': 8.640765919352019}, 
4680              - pA = 0.930027999814003, 
4681              - dw = 4.338620619954370, 
4682              - dwH = -0.274250775560818, 
4683              - kex = 344.613362916544475, 
4684              - chi2 = 10.367733168217050. 
4685          """ 
4686   
4687          # Base data setup. 
4688          self.setup_korzhnev_2005_data(data_list=['MQ']) 
4689   
4690          # Alias the spin. 
4691          spin = return_spin(":9@N") 
4692   
4693          # The R20 keys. 
4694          r20_key1 = generate_r20_key(exp_type=EXP_TYPE_CPMG_MQ, frq=500e6) 
4695          r20_key2 = generate_r20_key(exp_type=EXP_TYPE_CPMG_MQ, frq=600e6) 
4696          r20_key3 = generate_r20_key(exp_type=EXP_TYPE_CPMG_MQ, frq=800e6) 
4697   
4698          # Set the initial parameter values. 
4699          spin.r2 = {r20_key1: 6.02016436619016, r20_key2: 6.65421500772308, r20_key3: 8.6729591487622} 
4700          spin.pA = 0.930083249288083 
4701          spin.dw = 4.33890689462363 
4702          spin.dwH = -0.274316585638047 
4703          spin.kex = 344.329651956132 
4704   
4705          # Low precision optimisation. 
4706          self.interpreter.minimise.execute(min_algor='simplex', func_tol=1e-05, max_iter=1000) 
4707   
4708          # Monte Carlo simulations. 
4709          self.interpreter.monte_carlo.setup(number=2) 
4710          self.interpreter.monte_carlo.create_data(method='back_calc') 
4711          self.interpreter.monte_carlo.initial_values() 
4712          self.interpreter.minimise.execute(min_algor='simplex', max_iter=10) 
4713          self.interpreter.monte_carlo.error_analysis() 
4714   
4715          # Plot the dispersion curves. 
4716          self.interpreter.relax_disp.plot_disp_curves(dir=ds.tmpdir, force=True) 
4717   
4718          # Save the results. 
4719          self.interpreter.state.save('state', dir=ds.tmpdir, compress_type=1, force=True) 
4720   
4721          # Printout. 
4722          print("\n\nOptimised parameters:\n") 
4723          print("%-20s %-20s" % ("Parameter", "Value (:9)")) 
4724          print("%-20s %20.15g" % ("R2 (500 MHz)", spin.r2[r20_key1])) 
4725          print("%-20s %20.15g" % ("R2 (600 MHz)", spin.r2[r20_key2])) 
4726          print("%-20s %20.15g" % ("R2 (800 MHz)", spin.r2[r20_key3])) 
4727          print("%-20s %20.15g" % ("pA", spin.pA)) 
4728          print("%-20s %20.15g" % ("dw", spin.dw)) 
4729          print("%-20s %20.15g" % ("dwH", spin.dwH)) 
4730          print("%-20s %20.15g" % ("kex", spin.kex)) 
4731          print("%-20s %20.15g\n" % ("chi2", spin.chi2)) 
4732   
4733          # Checks for residue :9. 
4734          self.assertAlmostEqual(spin.r2[r20_key1], 6.02016436619016, 1) 
4735          self.assertAlmostEqual(spin.r2[r20_key2], 6.65421500772308, 1) 
4736          self.assertAlmostEqual(spin.r2[r20_key3], 8.6729591487622, 1) 
4737          self.assertAlmostEqual(spin.pA, 0.930083249288083, 3) 
4738          self.assertAlmostEqual(spin.dw, 4.33890689462363, 2) 
4739          self.assertAlmostEqual(spin.dwH, -0.274316585638047, 3) 
4740          self.assertAlmostEqual(spin.kex/1000, 344.329651956132/1000, 3) 
4741          self.assertAlmostEqual(spin.chi2, 10.3654315659173, 2) 
4742   
4743   
4744 -    def test_korzhnev_2005_15n_sq_data(self): 
4745          """Optimisation of the Korzhnev et al., 2005 15N SQ CPMG data using the 'NS MMQ 2-site' model. 
4746   
4747          This uses the data from Dmitry Korzhnev's paper at U{DOI: 10.1021/ja054550e<http://dx.doi.org/10.1021/ja054550e>}.  This is the 1H SQ, 15N SQ, ZQ, DQ, 1H MQ and 15N MQ data for residue Asp 9 of the Fyn SH3 domain mutant. 
4748   
4749          Here only the 15N SQ data will be optimised.  The values found by cpmg_fit using just this data are: 
4750   
4751              - r2 = {'500': 8.335037972570017, '600': 8.761366016417508, '800': 10.225001019091822}, 
4752              - pA = 0.950003458294991, 
4753              - dw = 4.358402855315123, 
4754              - kex = 429.906473361926999, 
4755              - chi2 = 17.393331915567252. 
4756          """ 
4757   
4758          # Base data setup. 
4759          self.setup_korzhnev_2005_data(data_list=['SQ']) 
4760   
4761          # Alias the spin. 
4762          spin = return_spin(":9@N") 
4763   
4764          # The R20 keys. 
4765          r20_key1 = generate_r20_key(exp_type=EXP_TYPE_CPMG_SQ, frq=500e6) 
4766          r20_key2 = generate_r20_key(exp_type=EXP_TYPE_CPMG_SQ, frq=600e6) 
4767          r20_key3 = generate_r20_key(exp_type=EXP_TYPE_CPMG_SQ, frq=800e6) 
4768   
4769          # Set the initial parameter values. 
4770          spin.r2 = {r20_key1: 8.334232330326190, r20_key2: 8.756773997879968, r20_key3: 10.219320492033058} 
4771          spin.pA = 0.950310172115387 
4772          spin.dw = 4.356737157889636 
4773          spin.kex = 433.176323890829849 
4774   
4775          # Low precision optimisation. 
4776          self.interpreter.minimise.execute(min_algor='simplex', func_tol=1e-05, max_iter=1000) 
4777   
4778          # Monte Carlo simulations. 
4779          self.interpreter.monte_carlo.setup(number=2) 
4780          self.interpreter.monte_carlo.create_data(method='back_calc') 
4781          self.interpreter.monte_carlo.initial_values() 
4782          self.interpreter.minimise.execute(min_algor='simplex', max_iter=10) 
4783          self.interpreter.monte_carlo.error_analysis() 
4784   
4785          # Plot the dispersion curves. 
4786          self.interpreter.relax_disp.plot_disp_curves(dir=ds.tmpdir, force=True) 
4787   
4788          # Save the results. 
4789          self.interpreter.state.save('state', dir=ds.tmpdir, compress_type=1, force=True) 
4790   
4791          # Printout. 
4792          print("\n\nOptimised parameters:\n") 
4793          print("%-20s %-20s" % ("Parameter", "Value (:9)")) 
4794          print("%-20s %20.15g" % ("R2 (500 MHz)", spin.r2[r20_key1])) 
4795          print("%-20s %20.15g" % ("R2 (600 MHz)", spin.r2[r20_key2])) 
4796          print("%-20s %20.15g" % ("R2 (800 MHz)", spin.r2[r20_key3])) 
4797          print("%-20s %20.15g" % ("pA", spin.pA)) 
4798          print("%-20s %20.15g" % ("dw", spin.dw)) 
4799          print("%-20s %20.15g" % ("kex", spin.kex)) 
4800          print("%-20s %20.15g\n" % ("chi2", spin.chi2)) 
4801   
4802          # Checks for residue :9. 
4803          self.assertAlmostEqual(spin.r2[r20_key1], 8.334232330326190, 2) 
4804          self.assertAlmostEqual(spin.r2[r20_key2], 8.756773997879968, 2) 
4805          self.assertAlmostEqual(spin.r2[r20_key3], 10.219320492033058, 1) 
4806          self.assertAlmostEqual(spin.pA, 0.950310172115387, 3) 
4807          self.assertAlmostEqual(spin.dw, 4.356737157889636, 2) 
4808          self.assertAlmostEqual(spin.kex/1000, 433.176323890829849/1000, 2) 
4809          self.assertAlmostEqual(spin.chi2, 17.37460582872912, 1) 
4810   
4811   
4812 -    def test_korzhnev_2005_15n_zq_data(self): 
4813          """Optimisation of the Korzhnev et al., 2005 15N ZQ CPMG data using the 'NS MMQ 2-site' model. 
4814   
4815          This uses the data from Dmitry Korzhnev's paper at U{DOI: 10.1021/ja054550e<http://dx.doi.org/10.1021/ja054550e>}.  This is the 1H SQ, 15N SQ, ZQ, DQ, 1H MQ and 15N MQ data for residue Asp 9 of the Fyn SH3 domain mutant. 
4816   
4817          Here only the 15N ZQ data will be optimised.  The values found by cpmg_fit using just this data are: 
4818   
4819              - r2 = {'500': 5.909812628572937, '600': 6.663690132557320, '800': 6.787171647689906}, 
4820              - pA = 0.942452612380140, 
4821              - dw = 0.858972784230892, 
4822              - dwH = 0.087155962730608, 
4823              - kex = 373.219151384798920, 
4824              - chi2 = 23.863208106025152. 
4825          """ 
4826   
4827          # Base data setup. 
4828          self.setup_korzhnev_2005_data(data_list=['ZQ']) 
4829   
4830          # Alias the spin. 
4831          spin = return_spin(":9@N") 
4832   
4833          # The R20 keys. 
4834          r20_key1 = generate_r20_key(exp_type=EXP_TYPE_CPMG_ZQ, frq=500e6) 
4835          r20_key2 = generate_r20_key(exp_type=EXP_TYPE_CPMG_ZQ, frq=600e6) 
4836          r20_key3 = generate_r20_key(exp_type=EXP_TYPE_CPMG_ZQ, frq=800e6) 
4837   
4838          # Set the initial parameter values. 
4839          spin.r2 = {r20_key1: 5.91033272691614, r20_key2: 6.66368695342258, r20_key3: 6.78922219135537} 
4840          spin.pA = 0.942457332074014 
4841          spin.dw = 0.850592422908884 
4842          spin.dwH = 0.0881272284455416 
4843          spin.kex = 372.745483351305 
4844   
4845          # Low precision optimisation. 
4846          self.interpreter.minimise.execute(min_algor='simplex', func_tol=1e-05, max_iter=1000) 
4847   
4848          # Monte Carlo simulations. 
4849          self.interpreter.monte_carlo.setup(number=2) 
4850          self.interpreter.monte_carlo.create_data(method='back_calc') 
4851          self.interpreter.monte_carlo.initial_values() 
4852          self.interpreter.minimise.execute(min_algor='simplex', max_iter=10) 
4853          self.interpreter.monte_carlo.error_analysis() 
4854   
4855          # Plot the dispersion curves. 
4856          self.interpreter.relax_disp.plot_disp_curves(dir=ds.tmpdir, force=True) 
4857   
4858          # Save the results. 
4859          self.interpreter.state.save('state', dir=ds.tmpdir, compress_type=1, force=True) 
4860   
4861          # Printout. 
4862          print("\n\nOptimised parameters:\n") 
4863          print("%-20s %-20s" % ("Parameter", "Value (:9)")) 
4864          print("%-20s %20.15g" % ("R2 (500 MHz)", spin.r2[r20_key1])) 
4865          print("%-20s %20.15g" % ("R2 (600 MHz)", spin.r2[r20_key2])) 
4866          print("%-20s %20.15g" % ("R2 (800 MHz)", spin.r2[r20_key3])) 
4867          print("%-20s %20.15g" % ("pA", spin.pA)) 
4868          print("%-20s %20.15g" % ("dw", spin.dw)) 
4869          print("%-20s %20.15g" % ("dwH", spin.dwH)) 
4870          print("%-20s %20.15g" % ("kex", spin.kex)) 
4871          print("%-20s %20.15g\n" % ("chi2", spin.chi2)) 
4872   
4873          # Checks for residue :9. 
4874          self.assertAlmostEqual(spin.r2[r20_key1], 5.91033272691614, 2) 
4875          self.assertAlmostEqual(spin.r2[r20_key2], 6.66368695342258, 2) 
4876          self.assertAlmostEqual(spin.r2[r20_key3], 6.78922219135537, 2) 
4877          self.assertAlmostEqual(spin.pA, 0.942457332074014, 4) 
4878          self.assertAlmostEqual(spin.dw, 0.850592422908884, 1) 
4879          self.assertAlmostEqual(spin.dwH, 0.0881272284455416, 2) 
4880          self.assertAlmostEqual(spin.kex/1000, 372.745483351305/1000, 3) 
4881          self.assertAlmostEqual(spin.chi2, 23.8464637019392, 1) 
4882   
4883   
4884 -    def test_korzhnev_2005_1h_mq_data(self): 
4885          """Optimisation of the Korzhnev et al., 2005 1H MQ CPMG data using the 'NS MMQ 2-site' model. 
4886   
4887          This uses the data from Dmitry Korzhnev's paper at U{DOI: 10.1021/ja054550e<http://dx.doi.org/10.1021/ja054550e>}.  This is the 1H SQ, 15N SQ, ZQ, DQ, 1H MQ and 15N MQ data for residue Asp 9 of the Fyn SH3 domain mutant. 
4888   
4889          Here only the 1H MQ data will be optimised.  The values found by cpmg_fit using just this data are: 
4890   
4891              - r2 = {'500': -0.000016676911302, '600': 0.036594127620440, '800': 2.131014839635728}, 
4892              - pA = 0.936911090448340, 
4893              - dw = 4.325314846914845, 
4894              - dwH = -0.213870168665628, 
4895              - kex = 487.361914835074117, 
4896              - chi2 = 14.870371897291138. 
4897          """ 
4898   
4899          # Base data setup. 
4900          self.setup_korzhnev_2005_data(data_list=['1H MQ']) 
4901   
4902          # Alias the spin. 
4903          spin = return_spin(":9@N") 
4904   
4905          # The R20 keys. 
4906          r20_key1 = generate_r20_key(exp_type=EXP_TYPE_CPMG_PROTON_MQ, frq=500e6) 
4907          r20_key2 = generate_r20_key(exp_type=EXP_TYPE_CPMG_PROTON_MQ, frq=600e6) 
4908          r20_key3 = generate_r20_key(exp_type=EXP_TYPE_CPMG_PROTON_MQ, frq=800e6) 
4909   
4910          # Set the initial parameter values. 
4911          spin.r2 = {r20_key1: 0.000022585022901, r20_key2: 0.039223196112941, r20_key3: 2.136576686700357} 
4912          spin.pA = 0.936884348941701 
4913          spin.dw = 4.326454531583964 
4914          spin.dwH = -0.214026093221782 
4915          spin.kex = 487.043592705469223 
4916   
4917          # Low precision optimisation. 
4918          self.interpreter.minimise.execute(min_algor='simplex', func_tol=1e-05, max_iter=100) 
4919   
4920          # Monte Carlo simulations. 
4921          self.interpreter.monte_carlo.setup(number=2) 
4922          self.interpreter.monte_carlo.create_data(method='back_calc') 
4923          self.interpreter.monte_carlo.initial_values() 
4924          self.interpreter.minimise.execute(min_algor='simplex', max_iter=10) 
4925          self.interpreter.monte_carlo.error_analysis() 
4926   
4927          # Plot the dispersion curves. 
4928          self.interpreter.relax_disp.plot_disp_curves(dir=ds.tmpdir, force=True) 
4929   
4930          # Save the results. 
4931          self.interpreter.state.save('state', dir=ds.tmpdir, compress_type=1, force=True) 
4932   
4933          # Printout. 
4934          print("\n\nOptimised parameters:\n") 
4935          print("%-20s %-20s" % ("Parameter", "Value (:9)")) 
4936          print("%-20s %20.15g" % ("R2 (500 MHz)", spin.r2[r20_key1])) 
4937          print("%-20s %20.15g" % ("R2 (600 MHz)", spin.r2[r20_key2])) 
4938          print("%-20s %20.15g" % ("R2 (800 MHz)", spin.r2[r20_key3])) 
4939          print("%-20s %20.15g" % ("pA", spin.pA)) 
4940          print("%-20s %20.15g" % ("dw", spin.dw)) 
4941          print("%-20s %20.15g" % ("dwH", spin.dwH)) 
4942          print("%-20s %20.15g" % ("kex", spin.kex)) 
4943          print("%-20s %20.15g\n" % ("chi2", spin.chi2)) 
4944   
4945          # Checks for residue :9. 
4946          self.assertAlmostEqual(spin.r2[r20_key1], 0.000023714274046, 4) 
4947          self.assertAlmostEqual(spin.r2[r20_key2], 0.039223196112941, 2) 
4948          self.assertAlmostEqual(spin.r2[r20_key3], 2.13657668670036, 2) 
4949          self.assertAlmostEqual(spin.pA, 0.936884348941701, 4) 
4950          self.assertAlmostEqual(spin.dw, 4.32645453158396, 2) 
4951          self.assertAlmostEqual(spin.dwH, -0.214026093221782, 2) 
4952          self.assertAlmostEqual(spin.kex/1000, 487.043592705469/1000, 4) 
4953          self.assertAlmostEqual(spin.chi2, 14.8642315375301, 2) 
4954   
4955   
4956 -    def test_korzhnev_2005_1h_sq_data(self): 
4957          """Optimisation of the Korzhnev et al., 2005 1H SQ CPMG data using the 'NS MMQ 2-site' model. 
4958   
4959          This uses the data from Dmitry Korzhnev's paper at U{DOI: 10.1021/ja054550e<http://dx.doi.org/10.1021/ja054550e>}.  This is the 1H SQ, 15N SQ, ZQ, DQ, 1H MQ and 15N MQ data for residue Asp 9 of the Fyn SH3 domain mutant. 
4960   
4961          Here only the 1H SQ data will be optimised.  The values found by cpmg_fit using just this data are: 
4962   
4963              - r2 = {'500': 6.691697587650816, '600': 6.998915158708793, '800': 5.519267837559072}, 
4964              - pA = 0.946949480545876, 
4965              - dwH = -0.265279672133308, 
4966              - kex = 406.548178869750700, 
4967              - chi2 = 50.400680290545026. 
4968          """ 
4969   
4970          # Base data setup. 
4971          self.setup_korzhnev_2005_data(data_list=['1H SQ']) 
4972   
4973          # Alias the spin. 
4974          spin = return_spin(":9@N") 
4975   
4976          # The R20 keys. 
4977          r20_key1 = generate_r20_key(exp_type=EXP_TYPE_CPMG_PROTON_SQ, frq=500e6) 
4978          r20_key2 = generate_r20_key(exp_type=EXP_TYPE_CPMG_PROTON_SQ, frq=600e6) 
4979          r20_key3 = generate_r20_key(exp_type=EXP_TYPE_CPMG_PROTON_SQ, frq=800e6) 
4980   
4981          # Set the initial parameter values. 
4982          spin.r2 = {r20_key1: 6.69107911078939, r20_key2: 6.99888898689085, r20_key3: 5.52012880268077} 
4983          spin.pA = 0.946990967372467 
4984          spin.dwH = -0.265308128403529 
4985          spin.kex = 406.843250675648 
4986   
4987          # Low precision optimisation. 
4988          self.interpreter.minimise.execute(min_algor='simplex', func_tol=1e-05, max_iter=1000) 
4989   
4990          # Monte Carlo simulations. 
4991          self.interpreter.monte_carlo.setup(number=2) 
4992          self.interpreter.monte_carlo.create_data(method='back_calc') 
4993          self.interpreter.monte_carlo.initial_values() 
4994          self.interpreter.minimise.execute(min_algor='simplex', max_iter=10) 
4995          self.interpreter.monte_carlo.error_analysis() 
4996   
4997          # Plot the dispersion curves. 
4998          self.interpreter.relax_disp.plot_disp_curves(dir=ds.tmpdir, force=True) 
4999   
5000          # Save the results. 
5001          self.interpreter.state.save('state', dir=ds.tmpdir, compress_type=1, force=True) 
5002   
5003          # Printout. 
5004          print("\n\nOptimised parameters:\n") 
5005          print("%-20s %-20s" % ("Parameter", "Value (:9)")) 
5006          print("%-20s %20.15g" % ("R2 (500 MHz)", spin.r2[r20_key1])) 
5007          print("%-20s %20.15g" % ("R2 (600 MHz)", spin.r2[r20_key2])) 
5008          print("%-20s %20.15g" % ("R2 (800 MHz)", spin.r2[r20_key3])) 
5009          print("%-20s %20.15g" % ("pA", spin.pA)) 
5010          print("%-20s %20.15g" % ("dwH", spin.dwH)) 
5011          print("%-20s %20.15g" % ("kex", spin.kex)) 
5012          print("%-20s %20.15g\n" % ("chi2", spin.chi2)) 
5013   
5014          # Checks for residue :9. 
5015          self.assertAlmostEqual(spin.r2[r20_key1], 6.69107911078939, 2) 
5016          self.assertAlmostEqual(spin.r2[r20_key2], 6.99888898689085, 2) 
5017          self.assertAlmostEqual(spin.r2[r20_key3], 5.52012880268077, 2) 
5018          self.assertAlmostEqual(spin.pA, 0.946990967372467, 4) 
5019          self.assertAlmostEqual(spin.dwH, -0.265308128403529, 3) 
5020          self.assertAlmostEqual(spin.kex/1000, 406.843250675648/1000, 2) 
5021          self.assertAlmostEqual(spin.chi2, 50.3431330819767, 1) 
5022   
5023   
5024 -    def test_korzhnev_2005_all_data(self): 
5025          """Optimisation of all the Korzhnev et al., 2005 CPMG data using the 'NS MMQ 2-site' model. 
5026   
5027          This uses the data from Dmitry Korzhnev's paper at U{DOI: 10.1021/ja054550e<http://dx.doi.org/10.1021/ja054550e>}.  This is the 1H SQ, 15N SQ, ZQ, DQ, 1H MQ and 15N MQ data for residue Asp 9 of the Fyn SH3 domain mutant. 
5028   
5029          Here all data will be optimised.  The values found by cpmg_fit using just this data are: 
5030   
5031              - r2 = {'H-S 500':  6.671649051677150, 'H-S 600':  6.988634195648529, 'H-S 800':  5.527971316790596, 
5032                      'N-S 500':  8.394988400015988, 'N-S 600':  8.891359568401835, 'N-S 800': 10.405356669006709, 
5033                      'NHZ 500':  5.936446687394352, 'NHZ 600':  6.717058062814535, 'NHZ 800':  6.838733853403030, 
5034                      'NHD 500':  8.593136215779710, 'NHD 600': 10.651511259239674, 'NHD 800': 12.567902357560627, 
5035                      'HNM 500':  7.851325614877817, 'HNM 600':  8.408803624020202, 'HNM 800': 11.227489645758979, 
5036                      'NHM 500':  9.189159145380575, 'NHM 600':  9.856814478405868, 'NHM 800': 11.967910041807118}, 
5037              - pA = 0.943125351763911, 
5038              - dw = 4.421827493809807, 
5039              - dwH = -0.272637034755752, 
5040              - kex = 360.609744568697238, 
5041              - chi2 = 162.589570340050813. 
5042          """ 
5043   
5044          # Base data setup. 
5045          self.setup_korzhnev_2005_data(data_list=['SQ', '1H SQ', 'DQ', 'ZQ', 'MQ', '1H MQ']) 
5046   
5047          # Alias the spin. 
5048          spin = return_spin(":9@N") 
5049   
5050          # The R20 keys. 
5051          r20_key1  = generate_r20_key(exp_type=EXP_TYPE_CPMG_PROTON_SQ, frq=500e6) 
5052          r20_key2  = generate_r20_key(exp_type=EXP_TYPE_CPMG_PROTON_SQ, frq=600e6) 
5053          r20_key3  = generate_r20_key(exp_type=EXP_TYPE_CPMG_PROTON_SQ, frq=800e6) 
5054          r20_key4  = generate_r20_key(exp_type=EXP_TYPE_CPMG_SQ, frq=500e6) 
5055          r20_key5  = generate_r20_key(exp_type=EXP_TYPE_CPMG_SQ, frq=600e6) 
5056          r20_key6  = generate_r20_key(exp_type=EXP_TYPE_CPMG_SQ, frq=800e6) 
5057          r20_key7  = generate_r20_key(exp_type=EXP_TYPE_CPMG_ZQ, frq=500e6) 
5058          r20_key8  = generate_r20_key(exp_type=EXP_TYPE_CPMG_ZQ, frq=600e6) 
5059          r20_key9  = generate_r20_key(exp_type=EXP_TYPE_CPMG_ZQ, frq=800e6) 
5060          r20_key10 = generate_r20_key(exp_type=EXP_TYPE_CPMG_DQ, frq=500e6) 
5061          r20_key11 = generate_r20_key(exp_type=EXP_TYPE_CPMG_DQ, frq=600e6) 
5062          r20_key12 = generate_r20_key(exp_type=EXP_TYPE_CPMG_DQ, frq=800e6) 
5063          r20_key13 = generate_r20_key(exp_type=EXP_TYPE_CPMG_PROTON_MQ, frq=500e6) 
5064          r20_key14 = generate_r20_key(exp_type=EXP_TYPE_CPMG_PROTON_MQ, frq=600e6) 
5065          r20_key15 = generate_r20_key(exp_type=EXP_TYPE_CPMG_PROTON_MQ, frq=800e6) 
5066          r20_key16 = generate_r20_key(exp_type=EXP_TYPE_CPMG_MQ, frq=500e6) 
5067          r20_key17 = generate_r20_key(exp_type=EXP_TYPE_CPMG_MQ, frq=600e6) 
5068          r20_key18 = generate_r20_key(exp_type=EXP_TYPE_CPMG_MQ, frq=800e6) 
5069   
5070          # Set the initial parameter values. 
5071          spin.r2 = { 
5072              r20_key1:   6.67288025927458, r20_key2:   6.98951408255098, r20_key3:   5.52959273852704, 
5073              r20_key4:   8.39471048876782, r20_key5:   8.89290699178799, r20_key6:  10.40770687236930, 
5074              r20_key7:   5.93611174376373, r20_key8:   6.71735669582514, r20_key9:   6.83835225518265, 
5075              r20_key10:  8.59615074668922, r20_key11: 10.65121378892910, r20_key12: 12.57108229191090, 
5076              r20_key13:  7.85956711501608, r20_key14:  8.41891642907918, r20_key15: 11.23620892230380, 
5077              r20_key16:  9.19654863789350, r20_key17:  9.86031627358462, r20_key18: 11.97523755925750 
5078          } 
5079          spin.pA = 0.943129019477673 
5080          spin.dw = 4.42209952545181 
5081          spin.dwH = -0.27258970590969 
5082          spin.kex = 360.516132791038 
5083   
5084          # Low precision optimisation. 
5085          self.interpreter.minimise.execute(min_algor='simplex', func_tol=1e-05, max_iter=10) 
5086   
5087          # Monte Carlo simulations. 
5088          self.interpreter.monte_carlo.setup(number=2) 
5089          self.interpreter.monte_carlo.create_data(method='back_calc') 
5090          self.interpreter.monte_carlo.initial_values() 
5091          self.interpreter.minimise.execute(min_algor='simplex', max_iter=10) 
5092          self.interpreter.monte_carlo.error_analysis() 
5093   
5094          # Plot the dispersion curves. 
5095          self.interpreter.relax_disp.plot_disp_curves(dir=ds.tmpdir, force=True) 
5096   
5097          # Save the results. 
5098          self.interpreter.state.save('state', dir=ds.tmpdir, compress_type=1, force=True) 
5099   
5100          # Printout. 
5101          print("\n\nOptimised parameters:\n") 
5102          print("%-20s %-20s" % ("Parameter", "Value (:9)")) 
5103          print("%-20s %20.15g" % ("R2 (1H SQ - 500 MHz)", spin.r2[r20_key1])) 
5104          print("%-20s %20.15g" % ("R2 (1H SQ - 600 MHz)", spin.r2[r20_key2])) 
5105          print("%-20s %20.15g" % ("R2 (1H SQ - 800 MHz)", spin.r2[r20_key3])) 
5106          print("%-20s %20.15g" % ("R2 (SQ - 500 MHz)", spin.r2[r20_key4])) 
5107          print("%-20s %20.15g" % ("R2 (SQ - 600 MHz)", spin.r2[r20_key5])) 
5108          print("%-20s %20.15g" % ("R2 (SQ - 800 MHz)", spin.r2[r20_key6])) 
5109          print("%-20s %20.15g" % ("R2 (ZQ - 500 MHz)", spin.r2[r20_key7])) 
5110          print("%-20s %20.15g" % ("R2 (ZQ - 600 MHz)", spin.r2[r20_key8])) 
5111          print("%-20s %20.15g" % ("R2 (ZQ - 800 MHz)", spin.r2[r20_key9])) 
5112          print("%-20s %20.15g" % ("R2 (DQ - 500 MHz)", spin.r2[r20_key10])) 
5113          print("%-20s %20.15g" % ("R2 (DQ - 600 MHz)", spin.r2[r20_key11])) 
5114          print("%-20s %20.15g" % ("R2 (DQ - 800 MHz)", spin.r2[r20_key12])) 
5115          print("%-20s %20.15g" % ("R2 (1H MQ - 500 MHz)", spin.r2[r20_key13])) 
5116          print("%-20s %20.15g" % ("R2 (1H MQ - 600 MHz)", spin.r2[r20_key14])) 
5117          print("%-20s %20.15g" % ("R2 (1H MQ - 800 MHz)", spin.r2[r20_key15])) 
5118          print("%-20s %20.15g" % ("R2 (MQ - 500 MHz)", spin.r2[r20_key16])) 
5119          print("%-20s %20.15g" % ("R2 (MQ - 600 MHz)", spin.r2[r20_key17])) 
5120          print("%-20s %20.15g" % ("R2 (MQ - 800 MHz)", spin.r2[r20_key18])) 
5121          print("%-20s %20.15g" % ("pA", spin.pA)) 
5122          print("%-20s %20.15g" % ("dw", spin.dw)) 
5123          print("%-20s %20.15g" % ("dwH", spin.dwH)) 
5124          print("%-20s %20.15g" % ("kex", spin.kex)) 
5125          print("%-20s %20.15g\n" % ("chi2", spin.chi2)) 
5126   
5127          # Checks for residue :9. 
5128          self.assertAlmostEqual(spin.r2[r20_key1],  6.67288025927458, 4) 
5129          self.assertAlmostEqual(spin.r2[r20_key2],  6.98951408255098, 4) 
5130          self.assertAlmostEqual(spin.r2[r20_key3],  5.52959273852704, 4) 
5131          self.assertAlmostEqual(spin.r2[r20_key4],  8.39471048876782, 4) 
5132          self.assertAlmostEqual(spin.r2[r20_key5],  8.89290699178799, 4) 
5133          self.assertAlmostEqual(spin.r2[r20_key6],  10.4077068723693, 4) 
5134          self.assertAlmostEqual(spin.r2[r20_key7],  5.93611174376373, 4) 
5135          self.assertAlmostEqual(spin.r2[r20_key8],  6.71735669582514, 4) 
5136          self.assertAlmostEqual(spin.r2[r20_key9],  6.83835225518265, 4) 
5137          self.assertAlmostEqual(spin.r2[r20_key10], 8.59615074668922, 4) 
5138          self.assertAlmostEqual(spin.r2[r20_key11], 10.6512137889291, 4) 
5139          self.assertAlmostEqual(spin.r2[r20_key12], 12.5710822919109, 4) 
5140          self.assertAlmostEqual(spin.r2[r20_key13], 7.85956711501608, 4) 
5141          self.assertAlmostEqual(spin.r2[r20_key14], 8.41891642907918, 4) 
5142          self.assertAlmostEqual(spin.r2[r20_key15], 11.2362089223038, 4) 
5143          self.assertAlmostEqual(spin.r2[r20_key16], 9.1965486378935, 4) 
5144          self.assertAlmostEqual(spin.r2[r20_key17], 9.86031627358462, 4) 
5145          self.assertAlmostEqual(spin.r2[r20_key18], 11.9752375592575, 4) 
5146          self.assertAlmostEqual(spin.pA, 0.943129019477673, 4) 
5147          self.assertAlmostEqual(spin.dw, 4.42209952545181, 4) 
5148          self.assertAlmostEqual(spin.dwH, -0.27258970590969, 4) 
5149          self.assertAlmostEqual(spin.kex/1000, 360.516132791038/1000, 4) 
5150          self.assertAlmostEqual(spin.chi2/1000, 162.511988511609/1000, 3) 
5151   
5152   
5153 -    def test_korzhnev_2005_all_data_disp_speed_bug(self): 
5154          """Optimisation of all the Korzhnev et al., 2005 CPMG data using the 'NS MMQ 2-site' model. 
5155   
5156          This uses the data from Dmitry Korzhnev's paper at U{DOI: 10.1021/ja054550e<http://dx.doi.org/10.1021/ja054550e>}.  This is the 1H SQ, 15N SQ, ZQ, DQ, 1H MQ and 15N MQ data for residue Asp 9 of the Fyn SH3 domain mutant. 
5157   
5158          Here all data will be optimised.  The values found by cpmg_fit using just this data are: 
5159   
5160              - r2 = {'H-S 500':  6.671649051677150, 'H-S 600':  6.988634195648529, 'H-S 800':  5.527971316790596, 
5161                      'N-S 500':  8.394988400015988, 'N-S 600':  8.891359568401835, 'N-S 800': 10.405356669006709, 
5162                      'NHZ 500':  5.936446687394352, 'NHZ 600':  6.717058062814535, 'NHZ 800':  6.838733853403030, 
5163                      'NHD 500':  8.593136215779710, 'NHD 600': 10.651511259239674, 'NHD 800': 12.567902357560627, 
5164                      'HNM 500':  7.851325614877817, 'HNM 600':  8.408803624020202, 'HNM 800': 11.227489645758979, 
5165                      'NHM 500':  9.189159145380575, 'NHM 600':  9.856814478405868, 'NHM 800': 11.967910041807118}, 
5166              - pA = 0.943125351763911, 
5167              - dw = 4.421827493809807, 
5168              - dwH = -0.272637034755752, 
5169              - kex = 360.609744568697238, 
5170              - chi2 = 162.589570340050813. 
5171          """ 
5172   
5173          # Base data setup. 
5174          self.setup_korzhnev_2005_data(data_list=['SQ', '1H SQ', 'DQ', 'ZQ', 'MQ', '1H MQ']) 
5175   
5176          # Alias the spin. 
5177          spin = return_spin(":9@N") 
5178   
5179          # The R20 keys. 
5180          r20_key1  = generate_r20_key(exp_type=EXP_TYPE_CPMG_PROTON_SQ, frq=500e6) 
5181          r20_key2  = generate_r20_key(exp_type=EXP_TYPE_CPMG_PROTON_SQ, frq=600e6) 
5182          r20_key3  = generate_r20_key(exp_type=EXP_TYPE_CPMG_PROTON_SQ, frq=800e6) 
5183          r20_key4  = generate_r20_key(exp_type=EXP_TYPE_CPMG_SQ, frq=500e6) 
5184          r20_key5  = generate_r20_key(exp_type=EXP_TYPE_CPMG_SQ, frq=600e6) 
5185          r20_key6  = generate_r20_key(exp_type=EXP_TYPE_CPMG_SQ, frq=800e6) 
5186          r20_key7  = generate_r20_key(exp_type=EXP_TYPE_CPMG_ZQ, frq=500e6) 
5187          r20_key8  = generate_r20_key(exp_type=EXP_TYPE_CPMG_ZQ, frq=600e6) 
5188          r20_key9  = generate_r20_key(exp_type=EXP_TYPE_CPMG_ZQ, frq=800e6) 
5189          r20_key10 = generate_r20_key(exp_type=EXP_TYPE_CPMG_DQ, frq=500e6) 
5190          r20_key11 = generate_r20_key(exp_type=EXP_TYPE_CPMG_DQ, frq=600e6) 
5191          r20_key12 = generate_r20_key(exp_type=EXP_TYPE_CPMG_DQ, frq=800e6) 
5192          r20_key13 = generate_r20_key(exp_type=EXP_TYPE_CPMG_PROTON_MQ, frq=500e6) 
5193          r20_key14 = generate_r20_key(exp_type=EXP_TYPE_CPMG_PROTON_MQ, frq=600e6) 
5194          r20_key15 = generate_r20_key(exp_type=EXP_TYPE_CPMG_PROTON_MQ, frq=800e6) 
5195          r20_key16 = generate_r20_key(exp_type=EXP_TYPE_CPMG_MQ, frq=500e6) 
5196          r20_key17 = generate_r20_key(exp_type=EXP_TYPE_CPMG_MQ, frq=600e6) 
5197          r20_key18 = generate_r20_key(exp_type=EXP_TYPE_CPMG_MQ, frq=800e6) 
5198   
5199          # Set the initial parameter values. 
5200          spin.r2 = { 
5201              r20_key1:   6.67288025927458, r20_key2:   6.98951408255098, r20_key3:   5.52959273852704, 
5202              r20_key4:   8.39471048876782, r20_key5:   8.89290699178799, r20_key6:  10.40770687236930, 
5203              r20_key7:   5.93611174376373, r20_key8:   6.71735669582514, r20_key9:   6.83835225518265, 
5204              r20_key10:  8.59615074668922, r20_key11: 10.65121378892910, r20_key12: 12.57108229191090, 
5205              r20_key13:  7.85956711501608, r20_key14:  8.41891642907918, r20_key15: 11.23620892230380, 
5206              r20_key16:  9.19654863789350, r20_key17:  9.86031627358462, r20_key18: 11.97523755925750 
5207          } 
5208          spin.pA = 0.943129019477673 
5209          spin.dw = 4.42209952545181 
5210          spin.dwH = -0.27258970590969 
5211          spin.kex = 360.516132791038 
5212   
5213          # Calc the chi2 values at these parameters. 
5214          self.interpreter.minimise.calculate(verbosity=1) 
5215   
5216          # Printout. 
5217          print("\n\nOptimised parameters:\n") 
5218          print("%-20s %-20s" % ("Parameter", "Value (:9)")) 
5219          print("%-20s %20.15g" % ("R2 (1H SQ - 500 MHz)", spin.r2[r20_key1])) 
5220          print("%-20s %20.15g" % ("R2 (1H SQ - 600 MHz)", spin.r2[r20_key2])) 
5221          print("%-20s %20.15g" % ("R2 (1H SQ - 800 MHz)", spin.r2[r20_key3])) 
5222          print("%-20s %20.15g" % ("R2 (SQ - 500 MHz)", spin.r2[r20_key4])) 
5223          print("%-20s %20.15g" % ("R2 (SQ - 600 MHz)", spin.r2[r20_key5])) 
5224          print("%-20s %20.15g" % ("R2 (SQ - 800 MHz)", spin.r2[r20_key6])) 
5225          print("%-20s %20.15g" % ("R2 (ZQ - 500 MHz)", spin.r2[r20_key7])) 
5226          print("%-20s %20.15g" % ("R2 (ZQ - 600 MHz)", spin.r2[r20_key8])) 
5227          print("%-20s %20.15g" % ("R2 (ZQ - 800 MHz)", spin.r2[r20_key9])) 
5228          print("%-20s %20.15g" % ("R2 (DQ - 500 MHz)", spin.r2[r20_key10])) 
5229          print("%-20s %20.15g" % ("R2 (DQ - 600 MHz)", spin.r2[r20_key11])) 
5230          print("%-20s %20.15g" % ("R2 (DQ - 800 MHz)", spin.r2[r20_key12])) 
5231          print("%-20s %20.15g" % ("R2 (1H MQ - 500 MHz)", spin.r2[r20_key13])) 
5232          print("%-20s %20.15g" % ("R2 (1H MQ - 600 MHz)", spin.r2[r20_key14])) 
5233          print("%-20s %20.15g" % ("R2 (1H MQ - 800 MHz)", spin.r2[r20_key15])) 
5234          print("%-20s %20.15g" % ("R2 (MQ - 500 MHz)", spin.r2[r20_key16])) 
5235          print("%-20s %20.15g" % ("R2 (MQ - 600 MHz)", spin.r2[r20_key17])) 
5236          print("%-20s %20.15g" % ("R2 (MQ - 800 MHz)", spin.r2[r20_key18])) 
5237          print("%-20s %20.15g" % ("pA", spin.pA)) 
5238          print("%-20s %20.15g" % ("dw", spin.dw)) 
5239          print("%-20s %20.15g" % ("dwH", spin.dwH)) 
5240          print("%-20s %20.15g" % ("kex", spin.kex)) 
5241          print("%-20s %20.15g\n" % ("chi2", spin.chi2)) 
5242   
5243          # Checks for residue :9. 
5244          self.assertAlmostEqual(spin.chi2/1000, 162.511988511609/1000, 3) 
5245   
5246   
5247 -    def test_kteilum_fmpoulsen_makke_check_graphs(self): 
5248          """Check of all possible dispersion graphs from optimisation of Kaare Teilum, Flemming M Poulsen, Mikael Akke 2006 "acyl-CoA binding protein" CPMG data to the CR72 dispersion model. 
5249   
5250          This uses the data from paper at U{http://dx.doi.org/10.1073/pnas.0509100103}.  This is CPMG data with a fixed relaxation time period.  Experiment in 0.48 M GuHCl (guanidine hydrochloride). 
5251   
5252          Figure 3 shows the ln( k_a [s^-1]) for different concentrations of GuHCl. The precise values are: 
5253   
5254            - [GuHCL][M] ln(k_a[s^-1]) k_a[s^-1] 
5255            - 0.483 0.89623903 2.4503699912708878 
5256            - 0.545 1.1694838 
5257            - 0.545 1.1761503 
5258            - 0.622 1.294 
5259            - 0.669 1.5176493 
5260            - 0.722 1.6238791 
5261            - 0.813 1.9395758 
5262            - 1.011 2.3558415 10.547000429321157 
5263          """ 
5264   
5265          # Base data setup. 
5266          model = 'TSMFK01' 
5267          expfolder = "acbp_cpmg_disp_048MGuHCl_40C_041223" 
5268          self.setup_kteilum_fmpoulsen_makke_cpmg_data(model=model, expfolder=expfolder) 
5269   
5270          # Alias the spins. 
5271          res61L = cdp.mol[0].res[0].spin[0] 
5272   
5273          # The R20 keys. 
5274          r20_key1 = generate_r20_key(exp_type=EXP_TYPE_CPMG_SQ, frq=599.89086220e6) 
5275   
5276          # Set the initial parameter values. 
5277          res61L.r2a = {r20_key1: 8.0} 
5278          res61L.dw = 6.5 
5279          res61L.k_AB = 2.5 
5280   
5281          # Low precision optimisation. 
5282          self.interpreter.minimise.execute(min_algor='simplex', line_search=None, hessian_mod=None, hessian_type=None, func_tol=1e-05, grad_tol=None, max_iter=1000, constraints=True, scaling=True, verbosity=1) 
5283   
5284          # Start testing all possible combinations of graphs. 
5285          y_axis_types = [Y_AXIS_R2_EFF, Y_AXIS_R2_R1RHO] 
5286          x_axis_types = [X_AXIS_DISP, X_AXIS_THETA, X_AXIS_W_EFF] 
5287          interpolate_types = [INTERPOLATE_DISP] 
5288   
5289          # Write to temp folder. 
5290          result_dir_name = ds.tmpdir 
5291          result_folders = [model] 
5292          spin_id = ":61@N" 
5293   
5294          # Loop through all possible combinations of y_axis, x_axis and interpolation. 
5295          data_path = status.install_path + sep+'test_suite'+sep+'shared_data'+sep+'dispersion'+sep+'KTeilum_FMPoulsen_MAkke_2006'+sep+expfolder+sep+'check_graphs' 
5296   
5297          for result_folder in result_folders: 
5298              for y_axis in y_axis_types: 
5299                  for x_axis in x_axis_types: 
5300                      for interpolate in interpolate_types: 
5301                          # Determine file name: 
5302                          file_name_ini = return_grace_file_name_ini(y_axis=y_axis, x_axis=x_axis, interpolate=interpolate) 
5303   
5304                          # Make the file name. 
5305                          file_name = "%s%s.agr" % (file_name_ini, spin_id.replace('#', '_').replace(':', '_').replace('@', '_')) 
5306   
5307                          # Write the curves. 
5308                          dir = result_dir_name+sep+result_folder 
5309                          print("Plotting combination of %s, %s, %s"%(y_axis, x_axis, interpolate)) 
5310                          self.interpreter.relax_disp.plot_disp_curves(dir=dir, y_axis=y_axis, x_axis=x_axis, interpolate=interpolate, force=True) 
5311   
5312                          # Get the file path. 
5313                          file_path = get_file_path(file_name, dir) 
5314   
5315                          # Test the plot file exists. 
5316                          print("Testing file access to graph: %s"%file_path) 
5317                          self.assert_(access(file_path, F_OK)) 
5318   
5319                          # Now open, and compare content, line by line. 
5320                          file_prod = open(file_path) 
5321                          lines_prod = file_prod.readlines() 
5322                          file_prod.close() 
5323   
5324                          # Define file to compare against. 
5325                          dir_comp = data_path+sep+result_folder 
5326                          file_path_comp = get_file_path(file_name, dir_comp) 
5327                          file_comp = open(file_path_comp) 
5328                          lines_comp = file_comp.readlines() 
5329                          file_comp.close() 
5330   
5331                          ## Assert number of lines is equal. 
5332                          self.assertEqual(len(lines_prod), len(lines_comp)) 
5333                          for j in range(len(lines_prod)): 
5334                              # Make the string test 
5335                              first_char = lines_prod[j][0] 
5336                              if first_char in ["@", "&"]: 
5337                                  self.assertEqual(lines_prod[j], lines_comp[j]) 
5338                              else: 
5339                                  # Split string in x, y, error. 
5340                                  # The error would change per run. 
5341                                  x_prod, y_prod, y_prod_err = lines_prod[j].split() 
5342                                  x_comp, y_comp, y_comp_err = lines_comp[j].split() 
5343                                  self.assertAlmostEqual(float(x_prod), float(x_comp)) 
5344                                  self.assertAlmostEqual(float(y_prod), float(y_comp)) 
5345                                  self.assertAlmostEqual(float(y_prod_err), float(y_comp_err)) 
5346   
5347   
5348 -    def test_kteilum_fmpoulsen_makke_cpmg_data_048m_guhcl_to_cr72(self): 
5349          """Optimisation of Kaare Teilum, Flemming M Poulsen, Mikael Akke 2006 "acyl-CoA binding protein" CPMG data to the CR72 dispersion model. 
5350   
5351          This uses the data from paper at U{http://dx.doi.org/10.1073/pnas.0509100103}.  This is CPMG data with a fixed relaxation time period.  Experiment in 0.48 M GuHCl (guanidine hydrochloride). 
5352          """ 
5353   
5354          # Base data setup. 
5355          self.setup_kteilum_fmpoulsen_makke_cpmg_data(model='CR72', expfolder="acbp_cpmg_disp_048MGuHCl_40C_041223") 
5356   
5357          # Alias the spins. 
5358          res61L = cdp.mol[0].res[0].spin[0] 
5359   
5360          # The R20 keys. 
5361          r20_key1 = generate_r20_key(exp_type=EXP_TYPE_CPMG_SQ, frq=599.89086220e6) 
5362   
5363          # Set the initial parameter values. 
5364          res61L.r2 = {r20_key1: 8.0} 
5365          res61L.pA = 0.9 
5366          res61L.dw = 6.0 
5367          res61L.kex = 600.0 
5368   
5369          # Low precision optimisation. 
5370          self.interpreter.minimise.execute(min_algor='simplex', line_search=None, hessian_mod=None, hessian_type=None, func_tol=1e-05, grad_tol=None, max_iter=1000, constraints=True, scaling=True, verbosity=1) 
5371   
5372          # Printout. 
5373          print("\n\nOptimised parameters:\n") 
5374          print("%-20s %-20s" % ("Parameter", "Value (:61)")) 
5375          print("%-20s %20.15g" % ("R2 (600 MHz)", res61L.r2[r20_key1])) 
5376          print("%-20s %20.15g" % ("pA", res61L.pA)) 
5377          print("%-20s %20.15g" % ("dw", res61L.dw)) 
5378          print("%-20s %20.15g" % ("kex", res61L.kex)) 
5379          print("%-20s %20.15g\n" % ("chi2", res61L.chi2)) 
5380   
5381          # Checks for residue :61. Calculated for 500 Monte Carlo simulations. 
5382          self.assertAlmostEqual(res61L.r2[r20_key1], 8.69277980194016, 4) 
5383          self.assertAlmostEqual(res61L.pA, 0.9943781590842946, 5) 
5384          self.assertAlmostEqual(res61L.dw, 6.389453131263374, 3) 
5385          self.assertAlmostEqual(res61L.kex, 609.262167216419, 0) 
5386          self.assertAlmostEqual(res61L.chi2, 65.99987828889657, 5) 
5387   
5388          # Test the conversion to k_AB from kex and pA. 
5389          self.assertEqual(res61L.k_AB, res61L.kex * (1.0 - res61L.pA)) 
5390   
5391          # Test the conversion to k_BA from kex and pA. 
5392          self.assertEqual(res61L.k_BA, res61L.kex * res61L.pA) 
5393   
5394   
5395 -    def test_kteilum_fmpoulsen_makke_cpmg_data_048m_guhcl_to_cr72_full(self): 
5396          """Optimisation of Kaare Teilum, Flemming M Poulsen, Mikael Akke 2006 "acyl-CoA binding protein" CPMG data to the CR72 dispersion model. 
5397   
5398          This uses the data from paper at U{http://dx.doi.org/10.1073/pnas.0509100103}.  This is CPMG data with a fixed relaxation time period.  Experiment in 0.48 M GuHCl (guanidine hydrochloride). 
5399          """ 
5400   
5401          # Base data setup. 
5402          self.setup_kteilum_fmpoulsen_makke_cpmg_data(model='CR72 full', expfolder="acbp_cpmg_disp_048MGuHCl_40C_041223") 
5403   
5404          # Alias the spins. 
5405          res61L = cdp.mol[0].res[0].spin[0] 
5406   
5407          # The R20 keys. 
5408          r20_key1 = generate_r20_key(exp_type=EXP_TYPE_CPMG_SQ, frq=599.89086220e6) 
5409   
5410          # Set the initial parameter values. 
5411          res61L.r2a = {r20_key1: 8.0} 
5412          res61L.r2b = {r20_key1: 105.0} 
5413          res61L.pA = 0.9 
5414          res61L.dw = 6.0 
5415          res61L.kex = 500.0 
5416   
5417          # Low precision optimisation. 
5418          self.interpreter.minimise.execute(min_algor='simplex', line_search=None, hessian_mod=None, hessian_type=None, func_tol=1e-05, grad_tol=None, max_iter=1000, constraints=True, scaling=True, verbosity=1) 
5419   
5420          # Printout. 
5421          print("\n\nOptimised parameters:\n") 
5422          print("%-20s %-20s" % ("Parameter", "Value (:61)")) 
5423          print("%-20s %20.15g" % ("R2A (600 MHz)", res61L.r2a[r20_key1])) 
5424          print("%-20s %20.15g" % ("R2B (600 MHz)", res61L.r2b[r20_key1])) 
5425          print("%-20s %20.15g" % ("pA", res61L.pA)) 
5426          print("%-20s %20.15g" % ("dw", res61L.dw)) 
5427          print("%-20s %20.15g" % ("kex", res61L.kex)) 
5428          print("%-20s %20.15g\n" % ("chi2", res61L.chi2)) 
5429   
5430          # Checks for residue :61. Calculated for 500 Monte Carlo simulations. 
5431          self.assertAlmostEqual(res61L.r2a[r20_key1], 8.044428899438309, 0) 
5432          self.assertAlmostEqual(res61L.r2b[r20_key1], 105.11894506392449, -2) 
5433          self.assertAlmostEqual(res61L.pA, 0.992066883657578, 2) 
5434          self.assertAlmostEqual(res61L.dw, 6.389453586338883, 3) 
5435          self.assertAlmostEqual(res61L.kex, 513.483608742063, -2) 
5436          self.assertAlmostEqual(res61L.chi2, 65.99987828890289, 5) 
5437   
5438   
5439 -    def test_kteilum_fmpoulsen_makke_cpmg_data_048m_guhcl_to_tsmfk01(self): 
5440          """Optimisation of Kaare Teilum, Flemming M Poulsen, Mikael Akke 2006 "acyl-CoA binding protein" CPMG data to the CR72 dispersion model. 
5441   
5442          This uses the data from paper at U{http://dx.doi.org/10.1073/pnas.0509100103}.  This is CPMG data with a fixed relaxation time period.  Experiment in 0.48 M GuHCl (guanidine hydrochloride). 
5443   
5444          Figure 3 shows the ln( k_a [s^-1]) for different concentrations of GuHCl. The precise values are: 
5445   
5446            - [GuHCL][M] ln(k_a[s^-1]) k_a[s^-1] 
5447            - 0.483 0.89623903 2.4503699912708878 
5448            - 0.545 1.1694838 
5449            - 0.545 1.1761503 
5450            - 0.622 1.294 
5451            - 0.669 1.5176493 
5452            - 0.722 1.6238791 
5453            - 0.813 1.9395758 
5454            - 1.011 2.3558415 10.547000429321157 
5455          """ 
5456   
5457          # Base data setup. 
5458          self.setup_kteilum_fmpoulsen_makke_cpmg_data(model='TSMFK01', expfolder="acbp_cpmg_disp_048MGuHCl_40C_041223") 
5459   
5460          # Alias the spins. 
5461          res61L = cdp.mol[0].res[0].spin[0] 
5462   
5463          # The R20 keys. 
5464          r20_key1 = generate_r20_key(exp_type=EXP_TYPE_CPMG_SQ, frq=599.89086220e6) 
5465   
5466          # Set the initial parameter values. 
5467          res61L.r2a = {r20_key1: 8.0} 
5468          res61L.dw = 6.5 
5469          res61L.k_AB = 2.5 
5470   
5471          # Low precision optimisation. 
5472          self.interpreter.minimise.execute(min_algor='simplex', line_search=None, hessian_mod=None, hessian_type=None, func_tol=1e-05, grad_tol=None, max_iter=1000, constraints=True, scaling=True, verbosity=1) 
5473   
5474          # Printout. 
5475          print("\n\nOptimised parameters:\n") 
5476          print("%-20s %-20s" % ("Parameter", "Value (:61)")) 
5477          print("%-20s %20.15g" % ("R2A (600 MHz)", res61L.r2a[r20_key1])) 
5478          print("%-20s %20.15g" % ("dw", res61L.dw)) 
5479          print("%-20s %20.15g" % ("k_AB", res61L.k_AB)) 
5480          print("%-20s %20.15g\n" % ("chi2", res61L.chi2)) 
5481   
5482          # Checks for residue :61. Reference values from paper 
5483   
5484          self.assertAlmostEqual(res61L.k_AB, 2.45, 1) 
5485   
5486   
5487 -    def test_kteilum_fmpoulsen_makke_cpmg_data_101m_guhcl_to_tsmfk01(self): 
5488          """Optimisation of Kaare Teilum, Flemming M Poulsen, Mikael Akke 2006 "acyl-CoA binding protein" CPMG data to the CR72 dispersion model. 
5489   
5490          This uses the data from paper at U{http://dx.doi.org/10.1073/pnas.0509100103}.  This is CPMG data with a fixed relaxation time period.  Experiment in 1.01 M GuHCl (guanidine hydrochloride). 
5491   
5492          The comparison is to Figure 2, which is for dataset with 1 M GuHCl.  The reported results are expected to be in rad.s^-1.  Conversion into relax stored values is preferably. 
5493   
5494          Representative 15N CPMG relaxation dispersion curve measured on the cross peaks from residue L61 in folded ACBP at pH 5.3, 1 M GuHCl, and 40C: 
5495   
5496            1. The dotted line represents a residue-specific fit of all parameters in Eq. 1: 
5497              - k_AB = 11.3 +/- 0.7 s^-1, 
5498              - dw = (2.45 +/- 0.09) * 10^3 s^-1, 
5499              - R2 = 8.0 +/- 0.5 s^-1. 
5500   
5501            2. The solid line represents a global fit of k_AB to all protein residues and a residue-specific fit of dw and R2.: 
5502              - k_AB = 10.55 +/- 0.08 s^-1, 
5503              - dw = (2.44 +/- 0.08) * 10^3 s^-1, 
5504              - R2 = 8.4 +/- 0.3 s^-1. 
5505   
5506          Conversion of paper results to relax results is performed by: 
5507   
5508            - dw(ppm) = dw(rad.s^-1) * 10^6 * 1/(2*pi) * (gyro1H/(gyro15N*spectrometer_freq)) = 2.45E3 * 1E6 / (2 * math.pi) * (26.7522212E7/(-2.7126E7 * 599.8908622E6)) = -6.41 ppm. 
5509   
5510          Figure 3 shows the ln( k_a [s^-1]) for different concentrations of GuHCl.  The precise values are: 
5511   
5512            - [GuHCL][M] ln(k_a[s^-1]) k_a[s^-1] 
5513            - 0.483 0.89623903 2.4503699912708878 
5514            - 0.545 1.1694838 
5515            - 0.545 1.1761503 
5516            - 0.622 1.294 
5517            - 0.669 1.5176493 
5518            - 0.722 1.6238791 
5519            - 0.813 1.9395758 
5520            - 1.011 2.3558415 10.547000429321157 
5521          """ 
5522   
5523          # Base data setup. 
5524          self.setup_kteilum_fmpoulsen_makke_cpmg_data(model='TSMFK01', expfolder="acbp_cpmg_disp_101MGuHCl_40C_041223") 
5525   
5526          # Alias the spins. 
5527          res61L = cdp.mol[0].res[0].spin[0] 
5528   
5529          # The R20 keys. 
5530          r20_key1 = generate_r20_key(exp_type=EXP_TYPE_CPMG_SQ, frq=599.89086270e6) 
5531   
5532          # Set the initial parameter values. 
5533          res61L.r2a = {r20_key1: 8.0} 
5534          res61L.dw = 6.5 
5535          res61L.k_AB = 11.0 
5536   
5537          # Low precision optimisation. 
5538          self.interpreter.minimise.execute(min_algor='simplex', line_search=None, hessian_mod=None, hessian_type=None, func_tol=1e-05, grad_tol=None, max_iter=1000, constraints=True, scaling=True, verbosity=1) 
5539   
5540          # Printout. 
5541          print("\n\nOptimised parameters:\n") 
5542          print("%-20s %-20s" % ("Parameter", "Value (:61)")) 
5543          print("%-20s %20.15g" % ("R2A (600 MHz)", res61L.r2a[r20_key1])) 
5544          print("%-20s %20.15g" % ("dw", res61L.dw)) 
5545          print("%-20s %20.15g" % ("k_AB", res61L.k_AB)) 
5546          print("%-20s %20.15g\n" % ("chi2", res61L.chi2)) 
5547   
5548          # Checks for residue :61. Reference values from paper 
5549   
5550          self.assertAlmostEqual(res61L.r2a[r20_key1], 8.4, 0) 
5551          self.assertAlmostEqual(res61L.dw, 6.41, 0) 
5552          self.assertAlmostEqual(res61L.k_AB, 10.55, 0) 
5553   
5554   
5555 -    def test_lm63_3site_synthetic(self): 
5556          """Test the 'LM63 3-site' dispersion model using the pure noise-free synthetic data.""" 
5557   
5558          # The path to the data files. 
5559          data_path = status.install_path + sep+'test_suite'+sep+'shared_data'+sep+'dispersion'+sep+'lm63_3site' 
5560   
5561          # Load the state file. 
5562          self.interpreter.reset() 
5563          self.interpreter.state.load(data_path+sep+'r2eff_values') 
5564   
5565          # A new data pipe. 
5566          self.interpreter.pipe.copy(pipe_from='base pipe', pipe_to='LM63 3-site', bundle_to='relax_disp') 
5567          self.interpreter.pipe.switch(pipe_name='LM63 3-site') 
5568   
5569          # Set up the model data. 
5570          self.interpreter.relax_disp.select_model(model='LM63 3-site') 
5571          self.interpreter.value.copy(pipe_from='R2eff - relax_disp', pipe_to='LM63 3-site', param='r2eff') 
5572          self.interpreter.spin.isotope('15N') 
5573   
5574          # Alias the spins. 
5575          spin1 = return_spin(":1") 
5576          spin2 = return_spin(":2") 
5577   
5578          # The R20 keys. 
5579          r20_key1 = generate_r20_key(exp_type=EXP_TYPE_CPMG_SQ, frq=500e6) 
5580          r20_key2 = generate_r20_key(exp_type=EXP_TYPE_CPMG_SQ, frq=800e6) 
5581   
5582          # Manually set the parameter values. 
5583          spin1.r2 = {r20_key1: 12.0, r20_key2: 12.0} 
5584          spin1.phi_ex_B = 0.1 
5585          spin1.phi_ex_C = 0.5 
5586          spin1.kB = 1500.0 
5587          spin1.kC = 2500.0 
5588          spin2.r2 = {r20_key1: 15.0, r20_key2: 15.0} 
5589          spin2.phi_ex_B = 0.1 
5590          spin2.phi_ex_C = 0.5 
5591          spin2.kB = 1500.0 
5592          spin2.kC = 2500.0 
5593   
5594          # Low precision optimisation. 
5595          self.interpreter.minimise.execute(min_algor='simplex', line_search=None, hessian_mod=None, hessian_type=None, func_tol=1e-05, grad_tol=None, max_iter=1000, constraints=True, scaling=True, verbosity=1) 
5596   
5597          # Monte Carlo simulations. 
5598          self.interpreter.monte_carlo.setup(number=3) 
5599          self.interpreter.monte_carlo.create_data(method='back_calc') 
5600          self.interpreter.monte_carlo.initial_values() 
5601          self.interpreter.minimise.execute(min_algor='simplex', line_search=None, hessian_mod=None, hessian_type=None, func_tol=1e-2, grad_tol=None, max_iter=10, constraints=True, scaling=True, verbosity=1) 
5602          self.interpreter.monte_carlo.error_analysis() 
5603   
5604          # Save the results. 
5605          self.interpreter.results.write(file='devnull', compress_type=1, force=True) 
5606   
5607          # The model checks. 
5608          print("\n\nOptimised parameters:\n") 
5609          print("%-20s %-20s %-20s" % ("Parameter", "Value (:1)", "Value (:2)")) 
5610          print("%-20s %20.15g %20.15g" % ("R2 (500 MHz)", spin1.r2[r20_key1], spin2.r2[r20_key1])) 
5611          print("%-20s %20.15g %20.15g" % ("R2 (800 MHz)", spin1.r2[r20_key2], spin2.r2[r20_key2])) 
5612          print("%-20s %20.15g %20.15g" % ("phi_ex_B", spin1.phi_ex_B, spin2.phi_ex_B)) 
5613          print("%-20s %20.15g %20.15g" % ("phi_ex_C", spin1.phi_ex_C, spin2.phi_ex_C)) 
5614          print("%-20s %20.15g %20.15g" % ("kB", spin1.kB, spin2.kB)) 
5615          print("%-20s %20.15g %20.15g" % ("kC", spin1.kC, spin2.kC)) 
5616          print("%-20s %20.15g %20.15g\n" % ("chi2", spin1.chi2, spin2.chi2)) 
5617          self.assertAlmostEqual(spin1.r2[r20_key1], 12.0, 2) 
5618          self.assertAlmostEqual(spin1.r2[r20_key2], 12.0, 2) 
5619          self.assertAlmostEqual(spin1.phi_ex_B, 0.1, 3) 
5620          self.assertAlmostEqual(spin1.phi_ex_C, 0.5, 3) 
5621          self.assertAlmostEqual(spin1.kB/1000, 1500.0/1000, 3) 
5622          self.assertAlmostEqual(spin1.kC/1000, 2500.0/1000, 3) 
5623          self.assertAlmostEqual(spin1.chi2, 0.0, 3) 
5624          self.assertAlmostEqual(spin2.r2[r20_key1], 15.0, 3) 
5625          self.assertAlmostEqual(spin2.r2[r20_key2], 15.0, 3) 
5626          self.assertAlmostEqual(spin1.phi_ex_B, 0.1, 3) 
5627          self.assertAlmostEqual(spin1.phi_ex_C, 0.5, 3) 
5628          self.assertAlmostEqual(spin1.kB/1000, 1500.0/1000, 3) 
5629          self.assertAlmostEqual(spin1.kC/1000, 2500.0/1000, 3) 
5630          self.assertAlmostEqual(spin2.chi2, 0.0, 3) 
5631   
5632   
5633 -    def test_m61_data_to_m61(self): 
5634          """Test the relaxation dispersion 'M61' model curve fitting to fixed time synthetic data.""" 
5635   
5636          # Fixed time variable. 
5637          ds.fixed = True 
5638   
5639          # Execute the script. 
5640          self.interpreter.run(script_file=status.install_path + sep+'test_suite'+sep+'system_tests'+sep+'scripts'+sep+'relax_disp'+sep+'r1rho_on_res_m61.py') 
5641   
5642          # The original parameters. 
5643          i0 = [100000.0, 20000.0] 
5644          r1rho_prime = [2.25, 24.0] 
5645          pA = 0.7 
5646          kex = 1000.0 
5647          delta_omega = [1.0, 2.0] 
5648          keys = ['r1rho_800.00000000_0.000_1000.000', 'r1rho_800.00000000_0.000_1500.000', 'r1rho_800.00000000_0.000_2000.000', 'r1rho_800.00000000_0.000_2500.000', 'r1rho_800.00000000_0.000_3000.000', 'r1rho_800.00000000_0.000_3500.000', 'r1rho_800.00000000_0.000_4000.000', 'r1rho_800.00000000_0.000_4500.000', 'r1rho_800.00000000_0.000_5000.000', 'r1rho_800.00000000_0.000_5500.000', 'r1rho_800.00000000_0.000_6000.000'] 
5649          phi_ex = [] 
5650          for i in range(2): 
5651              phi_ex.append(pA * (1.0 - pA) * delta_omega[i]**2) 
5652          rates = [[3.59768160399, 2.85730469783, 2.59328084312, 2.47019857325, 2.40310451058, 2.36256876552, 2.33622716364, 2.31815271355, 2.30521680479, 2.29564174079, 2.28835686631], [29.390726416, 26.4292187913, 25.3731233725, 24.880794293, 24.6124180423, 24.4502750621, 24.3449086546, 24.2726108542, 24.2208672192, 24.1825669632, 24.1534274652]] 
5653   
5654          # Switch to the 'R2eff' model data pipe, then check for each spin. 
5655          self.interpreter.pipe.switch('R2eff - relax_disp') 
5656          spin_index = 0 
5657          for spin, spin_id in spin_loop(return_id=True): 
5658              # Printout. 
5659              print("\nSpin %s." % spin_id) 
5660   
5661              # Check the fitted parameters. 
5662              for i in range(len(keys)): 
5663                  self.assertAlmostEqual(spin.r2eff[keys[i]]/10.0, rates[spin_index][i]/10.0, 2) 
5664   
5665              # Increment the spin index. 
5666              spin_index += 1 
5667   
5668          # The R20 keys. 
5669          r20_key1 = generate_r20_key(exp_type=EXP_TYPE_R1RHO, frq=800e6) 
5670   
5671          # Switch to the 'M61' model data pipe, then check for each spin. 
5672          self.interpreter.pipe.switch('M61 - relax_disp') 
5673          spin_index = 0 
5674          for spin, spin_id in spin_loop(return_id=True): 
5675              # Printout. 
5676              print("\nSpin %s." % spin_id) 
5677   
5678              # Check the fitted parameters. 
5679              self.assertAlmostEqual(spin.r2[r20_key1]/10, r1rho_prime[spin_index]/10, 2) 
5680              self.assertAlmostEqual(spin.phi_ex, phi_ex[spin_index], 2) 
5681              self.assertAlmostEqual(spin.kex/1000.0, kex/1000.0, 2) 
5682   
5683              # Increment the spin index. 
5684              spin_index += 1 
5685   
5686   
5687 -    def test_m61_exp_data_to_m61(self): 
5688          """Test the relaxation dispersion 'M61' model curve fitting to the full exponential synthetic data.""" 
5689   
5690          # Fixed time variable. 
5691          ds.fixed = False 
5692   
5693          # Single spin optimisation. 
5694          ds.single = True 
5695   
5696          # Execute the script. 
5697          self.interpreter.run(script_file=status.install_path + sep+'test_suite'+sep+'system_tests'+sep+'scripts'+sep+'relax_disp'+sep+'r1rho_on_res_m61.py') 
5698   
5699          # The original parameters. 
5700          i0 = [100000.0, 20000.0] 
5701          r1rho_prime = [2.25, 24.0] 
5702          pA = 0.7 
5703          kex = 1000.0 
5704          delta_omega = [1.0, 2.0] 
5705          keys = ['r1rho_800.00000000_0.000_1000.000', 'r1rho_800.00000000_0.000_1500.000', 'r1rho_800.00000000_0.000_2000.000', 'r1rho_800.00000000_0.000_2500.000', 'r1rho_800.00000000_0.000_3000.000', 'r1rho_800.00000000_0.000_3500.000', 'r1rho_800.00000000_0.000_4000.000', 'r1rho_800.00000000_0.000_4500.000', 'r1rho_800.00000000_0.000_5000.000', 'r1rho_800.00000000_0.000_5500.000', 'r1rho_800.00000000_0.000_6000.000'] 
5706          phi_ex = [] 
5707          for i in range(2): 
5708              phi_ex.append(pA * (1.0 - pA) * delta_omega[i]**2) 
5709          rates = [[3.59768160399, 2.85730469783, 2.59328084312, 2.47019857325, 2.40310451058, 2.36256876552, 2.33622716364, 2.31815271355, 2.30521680479, 2.29564174079, 2.28835686631], [29.390726416, 26.4292187913, 25.3731233725, 24.880794293, 24.6124180423, 24.4502750621, 24.3449086546, 24.2726108542, 24.2208672192, 24.1825669632, 24.1534274652]] 
5710   
5711          # Switch to the 'R2eff' model data pipe, then check for each spin. 
5712          self.interpreter.pipe.switch('R2eff - relax_disp') 
5713          spin_index = 0 
5714          for spin, spin_id in spin_loop(return_id=True): 
5715              # Printout. 
5716              print("\nSpin %s." % spin_id) 
5717   
5718              # Check the fitted parameters. 
5719              for i in range(len(keys)): 
5720                  self.assertAlmostEqual(spin.r2eff[keys[i]]/10.0, rates[spin_index][i]/10.0, 2) 
5721   
5722              # Increment the spin index. 
5723              spin_index += 1 
5724   
5725          # The R20 keys. 
5726          r20_key1 = generate_r20_key(exp_type=EXP_TYPE_R1RHO, frq=800e6) 
5727   
5728          # Switch to the 'M61' model data pipe, then check for each spin. 
5729          self.interpreter.pipe.switch('M61 - relax_disp') 
5730          spin_index = 0 
5731          for spin, spin_id in spin_loop(return_id=True): 
5732              # Printout. 
5733              print("\nSpin %s." % spin_id) 
5734   
5735              # Check the fitted parameters. 
5736              self.assertAlmostEqual(spin.r2[r20_key1]/10, r1rho_prime[spin_index]/10, 2) 
5737              self.assertAlmostEqual(spin.phi_ex, phi_ex[spin_index], 2) 
5738              self.assertAlmostEqual(spin.kex/1000.0, kex/1000.0, 2) 
5739   
5740              # Increment the spin index. 
5741              spin_index += 1 
5742   
5743   
5744 -    def xxx_test_m61b_data_to_m61b(self): 
5745          """Test the relaxation dispersion 'M61 skew' model curve fitting to fixed time synthetic data.""" 
5746   
5747          # Execute the script. 
5748          self.interpreter.run(script_file=status.install_path + sep+'test_suite'+sep+'system_tests'+sep+'scripts'+sep+'relax_disp'+sep+'r1rho_on_res_m61b.py') 
5749   
5750          # The original parameters. 
5751          i0 = [100000.0, 20000.0] 
5752          r1rho_prime = [10.0, 24.0] 
5753          pA = 0.95 
5754          kex = 2000.0 
5755          delta_omega = [1.0, 2.0] 
5756   
5757          # The R20 keys. 
5758          r20_key1 = generate_r20_key(exp_type=EXP_TYPE_R1RHO, frq=800e6) 
5759   
5760          # Switch to the 'M61 skew' model data pipe, then check for each spin. 
5761          self.interpreter.pipe.switch("%s - relax_disp" % MODEL_M61B) 
5762          spin_index = 0 
5763          for spin, spin_id in spin_loop(return_id=True): 
5764              # Printout. 
5765              print("\nSpin %s." % spin_id) 
5766   
5767              # Check the fitted parameters. 
5768              self.assertAlmostEqual(spin.r2[r20_key1]/10, r1rho_prime[spin_index]/10, 2) 
5769              self.assertAlmostEqual(spin.pA, pA, 2) 
5770              self.assertAlmostEqual(spin.dw, dw[spin_index], 2) 
5771              self.assertAlmostEqual(spin.kex/1000.0, kex/1000.0, 2) 
5772   
5773              # Increment the spin index. 
5774              spin_index += 1 
5775   
5776   
5777 -    def test_model_nesting_and_param(self): 
5778          """Test that all models which can nest, have all their parameters converted.""" 
5779   
5780          # Set the experiment type. 
5781          cdp.exp_type_list = EXP_TYPE_LIST 
5782   
5783          # Get info for all models. 
5784          all_models_info = models_info(models=MODEL_LIST_FULL) 
5785   
5786          # Loop over all models. 
5787          print("Printing the listed of nested models for each model.") 
5788          print("#########################################") 
5789          for model_info in all_models_info: 
5790              print("%s"%model_info.model), 
5791              print("<-"), 
5792              nest_list = model_info.nest_list 
5793              if nest_list == None: 
5794                  nest_list = ["None"] 
5795              print(', '.join(map(str, nest_list))) 
5796   
5797              # Skip if there is no model to nest from. 
5798              if nest_list == ["None"]: 
5799                  continue 
5800   
5801              # Assign params to variable. 
5802              model_params = model_info.params 
5803   
5804              # Now loop over the nested models. 
5805              for nested_model in nest_list: 
5806                  # Get the params for the nested model. 
5807                  nested_model_params = MODEL_PARAMS[nested_model] 
5808   
5809                  # Get the dictionary of parameter conversion. 
5810                  par_dic = nesting_param(model_params=model_params, nested_model_params=nested_model_params) 
5811   
5812                  # Test the number of elements in the dictionary. 
5813                  self.assertEqual(len(par_dic), len(model_params)) 
5814   
5815                  # Loop over dictionary. 
5816                  for param, param_conv in par_dic.iteritems(): 
5817                          if param != param_conv: 
5818                              print("Model:'%s', Nested model:'%s', Copying '%s' to '%s'." % (model_info.model, nested_model, param_conv, param)) 
5819                          self.assertNotEqual(param_conv, None) 
5820   
5821   
5822 -    def test_ns_mmq_3site(self): 
5823          """Compare the 'NS MMQ 3-site' dispersion model to synthetic data from cpmg_fit.""" 
5824   
5825          # Execute the script. 
5826          self.interpreter.run(script_file=status.install_path + sep+'test_suite'+sep+'system_tests'+sep+'scripts'+sep+'relax_disp'+sep+'ns_mmq_3site.py') 
5827   
5828          # Check the chi-squared value. 
5829          self.assertAlmostEqual(cdp.mol[0].res[0].spin[1].chi2, 0.0, 3) 
5830   
5831   
5832 -    def test_ns_mmq_3site_linear(self): 
5833          """Compare the 'NS MMQ 3-site linear' dispersion model to synthetic data from cpmg_fit.""" 
5834   
5835          # Execute the script. 
5836          self.interpreter.run(script_file=status.install_path + sep+'test_suite'+sep+'system_tests'+sep+'scripts'+sep+'relax_disp'+sep+'ns_mmq_3site_linear.py') 
5837   
5838          # Check the chi-squared value. 
5839          self.assertAlmostEqual(cdp.mol[0].res[0].spin[1].chi2, 0.0, 3) 
5840   
5841   
5842 -    def test_ns_r1rho_3site(self): 
5843          """Compare the 'NS R1rho 3-site' dispersion model to synthetic data from cpmg_fit.""" 
5844   
5845          # Execute the script. 
5846          self.interpreter.run(script_file=status.install_path + sep+'test_suite'+sep+'system_tests'+sep+'scripts'+sep+'relax_disp'+sep+'ns_r1rho_3site.py') 
5847   
5848          # Check the chi-squared value. 
5849          self.assertAlmostEqual(cdp.mol[0].res[0].spin[0].chi2, 136.13141468674999, 3) 
5850   
5851   
5852 -    def test_ns_r1rho_3site_linear(self): 
5853          """Compare the 'NS R1rho 3-site linear' dispersion model to synthetic data from cpmg_fit.""" 
5854   
5855          # Execute the script. 
5856          self.interpreter.run(script_file=status.install_path + sep+'test_suite'+sep+'system_tests'+sep+'scripts'+sep+'relax_disp'+sep+'ns_r1rho_3site_linear.py') 
5857   
5858          # Check the chi-squared value. 
5859          self.assertAlmostEqual(cdp.mol[0].res[0].spin[0].chi2, 0.030959849811015544, 3) 
5860   
5861   
5862 -    def test_r1rho_kjaergaard_auto(self): 
5863          """Optimisation of the Kjaergaard et al., 2013 Off-resonance R1rho relaxation dispersion experiments using the 'DPL' model. 
5864   
5865          This uses the data from Kjaergaard's paper at U{DOI: 10.1021/bi4001062<http://dx.doi.org/10.1021/bi4001062>}. 
5866   
5867          This uses the automatic analysis. 
5868   
5869          """ 
5870   
5871          # Cluster residues 
5872          cluster_ids = [ 
5873          ":13@N", 
5874          ":15@N", 
5875          ":16@N", 
5876          ":25@N", 
5877          ":26@N", 
5878          ":28@N", 
5879          ":39@N", 
5880          ":40@N", 
5881          ":41@N", 
5882          ":43@N", 
5883          ":44@N", 
5884          ":45@N", 
5885          ":49@N", 
5886          ":52@N", 
5887          ":53@N"] 
5888   
5889          # Load the data. 
5890          self.setup_r1rho_kjaergaard(cluster_ids=cluster_ids) 
5891   
5892          # Test some of the sequence. 
5893          self.assertEqual(len(cdp.mol), 1) 
5894          self.assertEqual(cdp.mol[0].name, None) 
5895          self.assertEqual(len(cdp.mol[0].res), 48) 
5896   
5897          # Test the chemical shift data. 
5898          cs = [122.223, 122.162, 114.250, 125.852, 118.626, 117.449, 119.999, 122.610, 118.602, 118.291, 115.393, 
5899          121.288, 117.448, 116.378, 116.316, 117.263, 122.211, 118.748, 118.103, 119.421, 119.317, 119.386, 117.279, 
5900          122.103, 120.038, 116.698, 111.811, 118.639, 118.285, 121.318, 117.770, 119.948, 119.759, 118.314, 118.160, 
5901          121.442, 118.714, 113.080, 125.706, 119.183, 120.966, 122.361, 126.675, 117.069, 120.875, 109.372, 119.811, 126.048] 
5902   
5903          i = 0 
5904          for spin, spin_id in spin_loop(return_id=True): 
5905              # Check the chemical shift. 
5906              self.assertEqual(spin.chemical_shift, cs[i]) 
5907   
5908              # Increment the index. 
5909              i += 1 
5910   
5911          # Initialize counter 
5912          i = 0 
5913          j = 0 
5914          # Count instances of select/deselect 
5915          for curspin, mol_name, res_num, res_name, spin_id in spin_loop(full_info=True, return_id=True, skip_desel=False): 
5916              if curspin.select == True: 
5917                  i += 1 
5918              if curspin.select == False: 
5919                  j += 1 
5920   
5921          # Test number of selected/deselected spins. 
5922          self.assertEqual(i, len(cluster_ids)) 
5923          self.assertEqual(j, 48-len(cluster_ids)) 
5924   
5925          # Check the initial setup. 
5926          self.assertEqual(cdp.mol[0].res[7].num, 13) 
5927          self.assertEqual(cdp.mol[0].res[7].spin[0].kex, ds.guess[':13@N'][6]) 
5928          self.assertEqual(cdp.mol[0].res[7].spin[0].ri_data['R1'], ds.ref[':13@N'][2]) 
5929   
5930          self.assertEqual(cdp.mol[0].res[9].num, 15) 
5931          self.assertEqual(cdp.mol[0].res[9].spin[0].kex, ds.guess[':15@N'][6]) 
5932          self.assertEqual(cdp.mol[0].res[9].spin[0].ri_data['R1'], ds.ref[':15@N'][2]) 
5933   
5934          self.assertEqual(cdp.mol[0].res[10].num, 16) 
5935          self.assertEqual(cdp.mol[0].res[10].spin[0].kex, ds.guess[':16@N'][6]) 
5936          self.assert_(hasattr(cdp.mol[0].res[10].spin[0], 'ri_data')) 
5937   
5938          self.assertEqual(cdp.mol[0].res[16].num, 25) 
5939          self.assertEqual(cdp.mol[0].res[16].spin[0].kex, ds.guess[':25@N'][6]) 
5940          self.assert_(hasattr(cdp.mol[0].res[16].spin[0], 'ri_data')) 
5941   
5942          self.assertEqual(cdp.mol[0].res[17].num, 26) 
5943          self.assertEqual(cdp.mol[0].res[17].spin[0].kex, ds.guess[':26@N'][6]) 
5944          self.assert_(hasattr(cdp.mol[0].res[17].spin[0], 'ri_data')) 
5945   
5946          self.assertEqual(cdp.mol[0].res[19].num, 28) 
5947          self.assertEqual(cdp.mol[0].res[19].spin[0].kex, ds.guess[':28@N'][6]) 
5948          self.assert_(hasattr(cdp.mol[0].res[19].spin[0], 'ri_data')) 
5949   
5950          self.assertEqual(cdp.mol[0].res[29].num, 39) 
5951          self.assertEqual(cdp.mol[0].res[29].spin[0].kex, ds.guess[':39@N'][6]) 
5952          self.assert_(hasattr(cdp.mol[0].res[29].spin[0], 'ri_data')) 
5953   
5954          self.assertEqual(cdp.mol[0].res[30].num, 40) 
5955          self.assertEqual(cdp.mol[0].res[30].spin[0].kex, ds.guess[':40@N'][6]) 
5956          self.assert_(hasattr(cdp.mol[0].res[30].spin[0], 'ri_data')) 
5957   
5958          self.assertEqual(cdp.mol[0].res[31].num, 41) 
5959          self.assertEqual(cdp.mol[0].res[31].spin[0].kex, ds.guess[':41@N'][6]) 
5960          self.assert_(hasattr(cdp.mol[0].res[31].spin[0], 'ri_data')) 
5961   
5962          self.assertEqual(cdp.mol[0].res[33].num, 43) 
5963          self.assertEqual(cdp.mol[0].res[33].spin[0].kex, ds.guess[':43@N'][6]) 
5964          self.assert_(hasattr(cdp.mol[0].res[33].spin[0], 'ri_data')) 
5965   
5966          self.assertEqual(cdp.mol[0].res[34].num, 44) 
5967          self.assertEqual(cdp.mol[0].res[34].spin[0].kex, ds.guess[':44@N'][6]) 
5968          self.assert_(hasattr(cdp.mol[0].res[34].spin[0], 'ri_data')) 
5969   
5970          self.assertEqual(cdp.mol[0].res[35].num, 45) 
5971          self.assertEqual(cdp.mol[0].res[35].spin[0].kex, ds.guess[':45@N'][6]) 
5972          self.assert_(hasattr(cdp.mol[0].res[35].spin[0], 'ri_data')) 
5973   
5974          self.assertEqual(cdp.mol[0].res[38].num, 49) 
5975          self.assertEqual(cdp.mol[0].res[38].spin[0].kex, ds.guess[':49@N'][6]) 
5976          self.assert_(hasattr(cdp.mol[0].res[38].spin[0], 'ri_data')) 
5977   
5978          self.assertEqual(cdp.mol[0].res[41].num, 52) 
5979          self.assertEqual(cdp.mol[0].res[41].spin[0].kex, ds.guess[':52@N'][6]) 
5980          self.assert_(hasattr(cdp.mol[0].res[41].spin[0], 'ri_data')) 
5981   
5982          self.assertEqual(cdp.mol[0].res[42].num, 53) 
5983          self.assertEqual(cdp.mol[0].res[42].spin[0].kex, ds.guess[':53@N'][6]) 
5984          self.assert_(hasattr(cdp.mol[0].res[42].spin[0], 'ri_data')) 
5985   
5986          # The dispersion models. 
5987          MODELS = [MODEL_R2EFF, MODEL_NOREX, MODEL_DPL94, MODEL_TP02, MODEL_TAP03, MODEL_MP05, MODEL_NS_R1RHO_2SITE] 
5988   
5989          # The grid search size (the number of increments per dimension). 
5990          GRID_INC = 4 
5991   
5992          # The number of Monte Carlo simulations to be used for error analysis at the end of the analysis. 
5993          MC_NUM = 3 
5994   
5995          # Model selection technique. 
5996          MODSEL = 'AIC' 
5997   
5998          # Execute the auto-analysis (fast). 
5999          # Standard parameters are: func_tol = 1e-25, grad_tol = None, max_iter = 10000000, 
6000          OPT_FUNC_TOL = 1e-1 
6001          relax_disp.Relax_disp.opt_func_tol = OPT_FUNC_TOL 
6002          OPT_MAX_ITERATIONS = 1000 
6003          relax_disp.Relax_disp.opt_max_iterations = OPT_MAX_ITERATIONS 
6004   
6005          result_dir_name = ds.tmpdir 
6006   
6007          # Make all spins free 
6008          for curspin in cluster_ids: 
6009              self.interpreter.relax_disp.cluster('free spins', curspin) 
6010              # Shut them down 
6011              self.interpreter.deselect.spin(spin_id=curspin, change_all=False) 
6012   
6013          # Select only a subset of spins for global fitting 
6014          #self.interpreter.select.spin(spin_id=':41@N', change_all=False) 
6015          #self.interpreter.relax_disp.cluster('model_cluster', ':41@N') 
6016   
6017          #self.interpreter.select.spin(spin_id=':40@N', change_all=False) 
6018          #self.interpreter.relax_disp.cluster('model_cluster', ':40@N') 
6019   
6020          self.interpreter.select.spin(spin_id=':52@N', change_all=False) 
6021          #self.interpreter.relax_disp.cluster('model_cluster', ':52@N') 
6022   
6023          # Run the analysis. 
6024          relax_disp.Relax_disp(pipe_name=ds.pipe_name, pipe_bundle=ds.pipe_bundle, results_dir=result_dir_name, models=MODELS, grid_inc=GRID_INC, mc_sim_num=MC_NUM, modsel=MODSEL) 
6025   
6026          # Check the kex value of residue 52 
6027          #self.assertAlmostEqual(cdp.mol[0].res[41].spin[0].kex, ds.ref[':52@N'][6]) 
6028   
6029          # Print results for each model. 
6030          print("\n\n################") 
6031          print("Printing results") 
6032          print("################\n") 
6033          for model in MODELS: 
6034              # Skip R2eff model. 
6035              if model == MODEL_R2EFF: 
6036                  continue 
6037   
6038              # Switch to pipe. 
6039              self.interpreter.pipe.switch(pipe_name='%s - relax_disp' % (model)) 
6040              print("\nModel: %s" % (model)) 
6041   
6042              # Loop over the spins. 
6043              for cur_spin, mol_name, resi, resn, spin_id in spin_loop(full_info=True, return_id=True, skip_desel=True): 
6044                  # Generate spin string. 
6045                  spin_string = generate_spin_string(spin=cur_spin, mol_name=mol_name, res_num=resi, res_name=resn) 
6046   
6047                  # Loop over the parameters. 
6048                  print("Optimised parameters for spin: %s" % (spin_string)) 
6049                  for param in cur_spin.params + ['chi2']: 
6050                      # Get the value. 
6051                      if param in ['r1', 'r2']: 
6052                          for exp_type, frq, ei, mi in loop_exp_frq(return_indices=True): 
6053                              # Generate the R20 key. 
6054                              r20_key = generate_r20_key(exp_type=exp_type, frq=frq) 
6055   
6056                              # Get the value. 
6057                              value = getattr(cur_spin, param)[r20_key] 
6058   
6059                              # Print value. 
6060                              print("%-10s %-6s %-6s %3.3f" % ("Parameter:", param, "Value:", value)) 
6061   
6062                      # For all other parameters. 
6063                      else: 
6064                          # Get the value. 
6065                          value = getattr(cur_spin, param) 
6066   
6067                          # Print value. 
6068                          print("%-10s %-6s %-6s %3.3f" % ("Parameter:", param, "Value:", value)) 
6069   
6070          # Print the final pipe. 
6071          self.interpreter.pipe.switch(pipe_name='%s - relax_disp' % ('final')) 
6072          print("\nFinal pipe") 
6073   
6074   
6075 -    def test_r1rho_kjaergaard_auto_check_graphs(self): 
6076          """Check of plot_disp_curves() function, after optimisation of the Kjaergaard et al., 2013 Off-resonance R1rho relaxation dispersion experiments using the 'R2eff' model. 
6077   
6078          This uses the data from Kjaergaard's paper at U{DOI: 10.1021/bi4001062<http://dx.doi.org/10.1021/bi4001062>}. 
6079   
6080          This uses the automatic analysis. 
6081   
6082          """ 
6083   
6084          # Cluster residues 
6085          cluster_ids = [ 
6086          ":52@N"] 
6087   
6088          # Load the data. 
6089          self.setup_r1rho_kjaergaard(cluster_ids=cluster_ids) 
6090   
6091          # The dispersion models. 
6092          MODELS = [MODEL_R2EFF] 
6093   
6094          # The grid search size (the number of increments per dimension). 
6095          GRID_INC = 4 
6096   
6097          # The number of Monte Carlo simulations to be used for error analysis at the end of the analysis. 
6098          MC_NUM = 3 
6099   
6100          # Model selection technique. 
6101          MODSEL = 'AIC' 
6102   
6103          # Execute the auto-analysis (fast). 
6104          # Standard parameters are: func_tol = 1e-25, grad_tol = None, max_iter = 10000000, 
6105          OPT_FUNC_TOL = 1e-1 
6106          relax_disp.Relax_disp.opt_func_tol = OPT_FUNC_TOL 
6107          OPT_MAX_ITERATIONS = 1000 
6108          relax_disp.Relax_disp.opt_max_iterations = OPT_MAX_ITERATIONS 
6109   
6110          result_dir_name = ds.tmpdir 
6111   
6112          # Make all spins free 
6113          for curspin in cluster_ids: 
6114              self.interpreter.relax_disp.cluster('free spins', curspin) 
6115              # Shut them down 
6116              self.interpreter.deselect.spin(spin_id=curspin, change_all=False) 
6117   
6118          self.interpreter.select.spin(spin_id=':52@N', change_all=False) 
6119   
6120          # Run the analysis. 
6121          relax_disp.Relax_disp(pipe_name=ds.pipe_name, pipe_bundle=ds.pipe_bundle, results_dir=result_dir_name, models=MODELS, grid_inc=GRID_INC, mc_sim_num=MC_NUM, modsel=MODSEL) 
6122   
6123          # Check the graphs produced. 
6124          graph_comb = [ 
6125          [Y_AXIS_R2_EFF, X_AXIS_DISP, INTERPOLATE_DISP], 
6126          [Y_AXIS_R2_EFF, X_AXIS_THETA, INTERPOLATE_DISP], 
6127          [Y_AXIS_R2_R1RHO, X_AXIS_W_EFF, INTERPOLATE_DISP], 
6128          [Y_AXIS_R2_EFF, X_AXIS_THETA, INTERPOLATE_OFFSET] 
6129          ] 
6130   
6131          # Define expected folder names. 
6132          result_folders = MODELS 
6133   
6134          # Assign spin_id. 
6135          spin_id = ':52@N' 
6136   
6137          # Loop over result folders. 
6138          for result_folder in result_folders: 
6139              # Skip the model R2eff, which does not produce graphs. 
6140              if result_folder == MODEL_R2EFF: 
6141                  continue 
6142   
6143              # Loop over graphs. 
6144              for y_axis, x_axis, interpolate in graph_comb: 
6145                  # Determine file name: 
6146                  file_name_ini = return_grace_file_name_ini(y_axis=y_axis, x_axis=x_axis, interpolate=interpolate) 
6147   
6148                  # Make the file name. 
6149                  file_name = "%s%s.agr" % (file_name_ini, spin_id.replace('#', '_').replace(':', '_').replace('@', '_')) 
6150   
6151                  # Get the file path. 
6152                  file_path = get_file_path(file_name, result_dir_name+sep+result_folder) 
6153   
6154                  print("Testing file access to graph: %s"%file_path) 
6155                  self.assert_(access(file_path, F_OK)) 
6156   
6157          # Start testing all possible combinations of graphs. 
6158          y_axis_types = [Y_AXIS_R2_EFF, Y_AXIS_R2_R1RHO] 
6159          x_axis_types = [X_AXIS_DISP, X_AXIS_THETA, X_AXIS_W_EFF] 
6160          interpolate_types = [INTERPOLATE_DISP, INTERPOLATE_OFFSET] 
6161   
6162          result_dir_name = ds.tmpdir 
6163   
6164          # Loop through all possible combinations of y_axis, x_axis and interpolation. 
6165          data_path = status.install_path + sep+'test_suite'+sep+'shared_data'+sep+'dispersion'+sep+'Kjaergaard_et_al_2013'+sep+'check_graphs' 
6166   
6167          for result_folder in result_folders: 
6168              # Skip the model R2eff, which does not produce graphs. 
6169              if result_folder == MODEL_R2EFF: 
6170                  continue 
6171   
6172              for y_axis in y_axis_types: 
6173                  for x_axis in x_axis_types: 
6174                      for interpolate in interpolate_types: 
6175                          # Determine file name: 
6176                          file_name_ini = return_grace_file_name_ini(y_axis=y_axis, x_axis=x_axis, interpolate=interpolate) 
6177   
6178                          # Make the file name. 
6179                          file_name = "%s%s.agr" % (file_name_ini, spin_id.replace('#', '_').replace(':', '_').replace('@', '_')) 
6180   
6181                          # Write the curves. 
6182                          dir = result_dir_name+sep+result_folder 
6183                          print("Plotting combination of %s, %s, %s"%(y_axis, x_axis, interpolate)) 
6184                          self.interpreter.relax_disp.plot_disp_curves(dir=dir, y_axis=y_axis, x_axis=x_axis, interpolate=interpolate, force=True) 
6185   
6186                          # Get the file path. 
6187                          file_path = get_file_path(file_name, dir) 
6188   
6189                          # Test the plot file exists. 
6190                          print("Testing file access to graph: %s"%file_path) 
6191                          self.assert_(access(file_path, F_OK)) 
6192   
6193                          # Now open, and compare content, line by line. 
6194                          file_prod = open(file_path) 
6195                          lines_prod = file_prod.readlines() 
6196                          file_prod.close() 
6197   
6198                          # Define file to compare against. 
6199                          dir_comp = data_path+sep+result_folder 
6200                          file_path_comp = get_file_path(file_name, dir_comp) 
6201                          file_comp = open(file_path_comp) 
6202                          lines_comp = file_comp.readlines() 
6203                          file_comp.close() 
6204   
6205                          # Assert number of lines is equal. 
6206                          self.assertEqual(len(lines_prod), len(lines_comp)) 
6207                          for j in range(len(lines_prod)): 
6208                              # Make the string test 
6209                              first_char = lines_prod[j][0] 
6210                              if first_char in ["@", "&"]: 
6211                                  self.assertEqual(lines_prod[j], lines_comp[j]) 
6212                              else: 
6213                                  # Split string in x, y, error. 
6214                                  # The error would change per run. 
6215                                  x_prod, y_prod, y_prod_err = lines_prod[j].split() 
6216                                  x_comp, y_comp, y_comp_err = lines_comp[j].split() 
6217                                  self.assertAlmostEqual(float(x_prod), float(x_comp)) 
6218                                  self.assertAlmostEqual(float(y_prod), float(y_comp)) 
6219   
6220   
6221 -    def test_r1rho_kjaergaard_missing_r1(self): 
6222          """Optimisation of the Kjaergaard et al., 2013 Off-resonance R1rho relaxation dispersion experiments using the 'DPL' model. 
6223   
6224          This uses the data from Kjaergaard's paper at U{DOI: 10.1021/bi4001062<http://dx.doi.org/10.1021/bi4001062>}. 
6225   
6226          This uses the automatic analysis, with missing loading R1. 
6227   
6228          """ 
6229   
6230          # Cluster residues 
6231          cluster_ids = [ 
6232          ":13@N", 
6233          ":15@N", 
6234          ":16@N", 
6235          ":25@N", 
6236          ":26@N", 
6237          ":28@N", 
6238          ":39@N", 
6239          ":40@N", 
6240          ":41@N", 
6241          ":43@N", 
6242          ":44@N", 
6243          ":45@N", 
6244          ":49@N", 
6245          ":52@N", 
6246          ":53@N"] 
6247   
6248          # Load the data. 
6249          self.setup_r1rho_kjaergaard(cluster_ids=cluster_ids, read_R1=False) 
6250   
6251          # The dispersion models. 
6252          MODELS = [MODEL_R2EFF, MODEL_NOREX, MODEL_DPL94, MODEL_TP02, MODEL_TAP03, MODEL_MP05, MODEL_NS_R1RHO_2SITE] 
6253   
6254          # The grid search size (the number of increments per dimension). 
6255          GRID_INC = None 
6256   
6257          # The number of Monte Carlo simulations to be used for error analysis at the end of the analysis. 
6258          MC_NUM = 3 
6259   
6260          # Model selection technique. 
6261          MODSEL = 'AIC' 
6262   
6263          # Execute the auto-analysis (fast). 
6264          # Standard parameters are: func_tol = 1e-25, grad_tol = None, max_iter = 10000000, 
6265          OPT_FUNC_TOL = 1e-25 
6266          relax_disp.Relax_disp.opt_func_tol = OPT_FUNC_TOL 
6267          OPT_MAX_ITERATIONS = 10000000 
6268          relax_disp.Relax_disp.opt_max_iterations = OPT_MAX_ITERATIONS 
6269   
6270          result_dir_name = ds.tmpdir 
6271   
6272          # Make all spins free 
6273          for curspin in cluster_ids: 
6274              self.interpreter.relax_disp.cluster('free spins', curspin) 
6275              # Shut them down 
6276              self.interpreter.deselect.spin(spin_id=curspin, change_all=False) 
6277   
6278          # Select only a subset of spins for global fitting 
6279          #self.interpreter.select.spin(spin_id=':41@N', change_all=False) 
6280          #self.interpreter.relax_disp.cluster('model_cluster', ':41@N') 
6281   
6282          #self.interpreter.select.spin(spin_id=':40@N', change_all=False) 
6283          #self.interpreter.relax_disp.cluster('model_cluster', ':40@N') 
6284   
6285          self.interpreter.select.spin(spin_id=':52@N', change_all=False) 
6286          #self.interpreter.relax_disp.cluster('model_cluster', ':52@N') 
6287   
6288          # Point to directory with R2eff values, with 2000 MC simulations. 
6289          prev_data_path = status.install_path + sep+'test_suite'+sep+'shared_data'+sep+'dispersion'+sep+'Kjaergaard_et_al_2013' +sep+ "check_graphs" +sep+ "mc_2000" 
6290   
6291          r1_fit = True 
6292   
6293          # Run the analysis. 
6294          relax_disp.Relax_disp(pipe_name=ds.pipe_name, pipe_bundle=ds.pipe_bundle, results_dir=result_dir_name, models=MODELS, grid_inc=GRID_INC, mc_sim_num=MC_NUM, modsel=MODSEL, pre_run_dir=prev_data_path, r1_fit=r1_fit) 
6295   
6296          # Verify the data. 
6297          self.verify_r1rho_kjaergaard_missing_r1(models=MODELS, result_dir_name=result_dir_name, r2eff_estimate='MC2000') 
6298   
6299   
6300 -    def test_r2eff_read(self): 
6301          """Test the operation of the relax_disp.r2eff_read user function.""" 
6302   
6303          # The path to the data files. 
6304          data_path = status.install_path + sep+'test_suite'+sep+'shared_data'+sep+'dispersion'+sep+'Hansen'+sep+'800_MHz' 
6305   
6306          # Read the sequence data. 
6307          self.interpreter.sequence.read(file='66.667.in', dir=data_path, res_num_col=1) 
6308   
6309          # The ID. 
6310          id = 'test' 
6311   
6312          # Set up the metadata. 
6313          self.interpreter.spectrometer.frequency(id=id, frq=800e6) 
6314          self.interpreter.relax_disp.exp_type(spectrum_id=id, exp_type='SQ CPMG') 
6315   
6316          # Try reading the file. 
6317          self.interpreter.relax_disp.r2eff_read(id=id, file='66.667.in', dir=data_path, disp_frq=66.667, res_num_col=1, data_col=2, error_col=3) 
6318   
6319          # Check the global data. 
6320          data = [ 
6321              ['cpmg_frqs', {'test': 66.667}], 
6322              ['cpmg_frqs_list', [66.667]], 
6323              ['dispersion_points', 1], 
6324              ['exp_type', {'test': 'SQ CPMG'}], 
6325              ['exp_type_list', ['SQ CPMG']], 
6326              ['spectrometer_frq', {'test': 800000000.0}], 
6327              ['spectrometer_frq_count', 1], 
6328              ['spectrometer_frq_list', [800000000.0]], 
6329              ['spectrum_ids', ['test']] 
6330          ] 
6331          for name, value in data: 
6332              # Does it exist? 
6333              self.assert_(hasattr(cdp, name)) 
6334   
6335              # Check the object. 
6336              obj = getattr(cdp, name) 
6337              self.assertEqual(obj, value) 
6338   
6339          # Check the spin data. 
6340          data = [ 
6341              [1,       2.3035747e+04, 8.5467725e+01], 
6342              [2,       9.9629762e+04, 2.8322033e+02], 
6343              [3,       9.5663137e+04, 2.8632929e+02], 
6344              [4,       1.7089893e+05, 3.1089428e+02], 
6345              [5,       4.7323876e+04, 1.0084269e+02], 
6346              [6,       2.0199122e+04, 1.0135220e+02], 
6347              [7,       1.6655488e+05, 3.1609061e+02], 
6348              [8,       9.0061074e+04, 1.9176585e+02], 
6349              [10,      8.4726204e+04, 2.8898155e+02], 
6350              [11,      1.5050233e+05, 4.3138029e+02], 
6351              [12,      9.2998531e+04, 3.0440191e+02], 
6352              [13,      1.6343507e+05, 3.3144097e+02], 
6353              [14,      1.0137301e+05, 3.7314642e+02], 
6354              [15,      8.3407837e+04, 1.6546473e+02], 
6355              [16,      1.3819126e+05, 3.3388517e+02], 
6356              [17,      1.1010490e+05, 3.5639222e+02], 
6357              [18,      9.4324035e+04, 3.2343585e+02], 
6358              [19,      1.1135179e+05, 3.0706671e+02], 
6359              [20,      7.6339410e+04, 1.7377460e+02], 
6360              [21,      6.2008453e+04, 1.7327150e+02], 
6361              [22,      1.0590404e+05, 2.4814635e+02], 
6362              [23,      1.0630198e+05, 2.3601100e+02], 
6363              [24,      7.2996320e+04, 1.4952465e+02], 
6364              [25,      9.5486742e+04, 2.7080766e+02], 
6365              [26,      5.8067989e+04, 1.6820462e+02], 
6366              [27,     -1.7168510e+04, 2.2519560e+02], 
6367              [28,      1.6891473e+05, 2.3497525e+02], 
6368              [29,      9.4038555e+04, 2.0357593e+02], 
6369              [30,      2.1386951e+04, 2.2153532e+02], 
6370              [31,      9.3982899e+04, 2.0937056e+02], 
6371              [32,      8.6097484e+04, 2.3868467e+02], 
6372              [33,      1.0194337e+05, 2.7370704e+02], 
6373              [34,      8.5683111e+04, 2.0838076e+02], 
6374              [35,      8.6985768e+04, 2.0889310e+02], 
6375              [36,      8.6011237e+04, 1.7498390e+02], 
6376              [37,      1.0984097e+05, 2.7622998e+02], 
6377              [38,      8.7017879e+04, 2.6547994e+02], 
6378              [39,      9.1682649e+04, 5.2777676e+02], 
6379              [40,      7.6370440e+04, 1.9873214e+02], 
6380              [41,      9.1393531e+04, 2.4483824e+02], 
6381              [42,      1.1017111e+05, 2.8020699e+02], 
6382              [43,      9.4552366e+04, 3.4394150e+02], 
6383              [44,      1.2858281e+05, 6.8449252e+02], 
6384              [45,      7.4583525e+04, 1.9544210e+02], 
6385              [46,      9.2087490e+04, 2.0491066e+02], 
6386              [47,      9.7507255e+04, 2.5162839e+02], 
6387              [48,      1.0033842e+05, 2.7566430e+02], 
6388              [49,      1.3048305e+05, 2.6797466e+02], 
6389              [50,      1.0546796e+05, 1.9304384e+02], 
6390              [51,      9.3099697e+04, 2.0773311e+02], 
6391              [52,      4.6863758e+04, 1.3169068e+02], 
6392              [53,      6.1055806e+04, 1.5448477e+02], 
6393              [55,      6.8629994e+04, 1.6868673e+02], 
6394              [56,      1.1005552e+05, 2.1940465e+02], 
6395              [57,      1.0572760e+05, 1.9768486e+02], 
6396              [58,      1.1176950e+05, 3.0009610e+02], 
6397              [59,      9.8758603e+04, 3.3803895e+02], 
6398              [60,      9.9517201e+04, 3.5137994e+02], 
6399              [61,      5.4357946e+04, 2.5896579e+02], 
6400              [62,      1.0899978e+05, 2.8720371e+02], 
6401              [63,      8.4549759e+04, 4.1401837e+02], 
6402              [64,      5.5014550e+04, 2.1135781e+02], 
6403              [65,      8.0569666e+04, 2.3249709e+02], 
6404              [66,      1.2936610e+05, 3.5218725e+02], 
6405              [67,      3.6438010e+04, 8.7924003e+01], 
6406              [70,      3.8763157e+04, 1.3325040e+02], 
6407              [71,      8.5711411e+04, 2.9316183e+02], 
6408              [72,      3.3211541e+04, 1.2182123e+02], 
6409              [73,      3.2070576e+04, 1.2305430e+02] 
6410          ] 
6411          for res_num, value, error in data: 
6412              # Get the spin. 
6413              spin = return_spin(spin_id=":%s"%res_num) 
6414   
6415              # Check the values. 
6416              self.assertEqual(spin.r2eff['sq_cpmg_800.00000000_0.000_66.667'], value) 
6417              self.assertEqual(spin.r2eff_err['sq_cpmg_800.00000000_0.000_66.667'], error) 
6418   
6419   
6420 -    def test_r2eff_read_spin(self): 
6421          """Test the operation of the relax_disp.r2eff_read_spin user function.""" 
6422   
6423          # The path to the data files. 
6424          data_path = status.install_path + sep+'test_suite'+sep+'shared_data'+sep+'dispersion'+sep+'Korzhnev_et_al_2005' 
6425   
6426          # Generate the sequence. 
6427          self.interpreter.spin.create(res_name='Asp', res_num=9, spin_name='H') 
6428          self.interpreter.spin.create(res_name='Asp', res_num=9, spin_name='N') 
6429          self.interpreter.spin.isotope('1H', spin_id='@H') 
6430          self.interpreter.spin.isotope('15N', spin_id='@N') 
6431   
6432          # Build the experiment IDs. 
6433          H_disp_points = [67.0, 133.0, 267.0, 400.0, 533.0, 667.0, 800.0, 933.0, 1067.0, 1600.0, 2133.0, 2667.0] 
6434          N_disp_points = [50.0, 100.0, 150.0, 200.0, 250.0, 300.0, 350.0, 400.0, 500.0, 600.0, 700.0, 800.0, 900.0, 1000.0] 
6435          ids = [] 
6436          for value in H_disp_points: 
6437              ids.append('1H_CPMG_%s' % value) 
6438          for value in N_disp_points: 
6439              ids.append('15N_CPMG_%s' % value) 
6440          print("\n\nThe experiment IDs are %s." % ids) 
6441   
6442          # Set up the metadata for the experiments. 
6443          for id in ids: 
6444              self.interpreter.spectrometer.frequency(id=id, frq=500e6) 
6445              self.interpreter.relax_disp.exp_type(spectrum_id=id, exp_type='SQ CPMG') 
6446          for value in H_disp_points: 
6447              self.interpreter.relax_disp.cpmg_setup(spectrum_id='1H_CPMG_%s' % value, cpmg_frq=value) 
6448          for value in N_disp_points: 
6449              self.interpreter.relax_disp.cpmg_setup(spectrum_id='15N_CPMG_%s' % value, cpmg_frq=value) 
6450   
6451          # Loop over the experiments. 
6452          for id, file, spin_id in [['1H_CPMG', 'hs_500.res', ':9@H'], ['15N_CPMG', 'ns_500.res', ':9@N']]: 
6453              # Try reading the file. 
6454              self.interpreter.relax_disp.r2eff_read_spin(id=id, file=file, dir=data_path, spin_id=spin_id, disp_point_col=1, data_col=2, error_col=3) 
6455   
6456          # Check the global data. 
6457          data = [ 
6458              ['cpmg_frqs', {'1H_CPMG_667.0': 667.0, '1H_CPMG_1067.0': 1067.0, '15N_CPMG_350.0': 350.0, '1H_CPMG_933.0': 933.0, '15N_CPMG_50.0': 50.0, '15N_CPMG_100.0': 100.0, '1H_CPMG_400.0': 400.0, '1H_CPMG_533.0': 533.0, '1H_CPMG_800.0': 800.0, '15N_CPMG_900.0': 900.0, '15N_CPMG_150.0': 150.0, '15N_CPMG_800.0': 800.0, '1H_CPMG_267.0': 267.0, '1H_CPMG_2667.0': 2667.0, '15N_CPMG_300.0': 300.0, '1H_CPMG_133.0': 133.0, '15N_CPMG_700.0': 700.0, '1H_CPMG_67.0': 67.0, '15N_CPMG_400.0': 400.0, '15N_CPMG_250.0': 250.0, '1H_CPMG_2133.0': 2133.0, '1H_CPMG_1600.0': 1600.0, '15N_CPMG_200.0': 200.0, '15N_CPMG_1000.0': 1000.0, '15N_CPMG_500.0': 500.0, '15N_CPMG_600.0': 600.0}], 
6459              ['cpmg_frqs_list', [50.0, 67.0, 100.0, 133.0, 150.0, 200.0, 250.0, 267.0, 300.0, 350.0, 400.0, 500.0, 533.0, 600.0, 667.0, 700.0, 800.0, 900.0, 933.0, 1000.0, 1067.0, 1600.0, 2133.0, 2667.0]], 
6460              ['dispersion_points', 24], 
6461              ['exp_type', {'1H_CPMG_667.0': 'SQ CPMG', '1H_CPMG_1067.0': 'SQ CPMG', '15N_CPMG_350.0': 'SQ CPMG', '1H_CPMG_933.0': 'SQ CPMG', '15N_CPMG_50.0': 'SQ CPMG', '15N_CPMG_100.0': 'SQ CPMG', '1H_CPMG_400.0': 'SQ CPMG', '1H_CPMG_533.0': 'SQ CPMG', '1H_CPMG_800.0': 'SQ CPMG', '15N_CPMG_900.0': 'SQ CPMG', '15N_CPMG_150.0': 'SQ CPMG', '15N_CPMG_800.0': 'SQ CPMG', '1H_CPMG_267.0': 'SQ CPMG', '1H_CPMG_2667.0': 'SQ CPMG', '15N_CPMG_300.0': 'SQ CPMG', '1H_CPMG_133.0': 'SQ CPMG', '15N_CPMG_700.0': 'SQ CPMG', '1H_CPMG_67.0': 'SQ CPMG', '15N_CPMG_400.0': 'SQ CPMG', '15N_CPMG_250.0': 'SQ CPMG', '1H_CPMG_2133.0': 'SQ CPMG', '1H_CPMG_1600.0': 'SQ CPMG', '15N_CPMG_200.0': 'SQ CPMG', '15N_CPMG_1000.0': 'SQ CPMG', '15N_CPMG_500.0': 'SQ CPMG', '15N_CPMG_600.0': 'SQ CPMG'}], 
6462              ['exp_type_list', ['SQ CPMG']], 
6463              ['spectrometer_frq', {'1H_CPMG_667.0': 500000000.0, '1H_CPMG_1067.0': 500000000.0, '15N_CPMG_350.0': 500000000.0, '1H_CPMG_933.0': 500000000.0, '15N_CPMG_50.0': 500000000.0, '15N_CPMG_100.0': 500000000.0, '1H_CPMG_400.0': 500000000.0, '1H_CPMG_533.0': 500000000.0, '1H_CPMG_800.0': 500000000.0, '15N_CPMG_900.0': 500000000.0, '15N_CPMG_150.0': 500000000.0, '15N_CPMG_800.0': 500000000.0, '1H_CPMG_267.0': 500000000.0, '1H_CPMG_2667.0': 500000000.0, '15N_CPMG_300.0': 500000000.0, '1H_CPMG_133.0': 500000000.0, '15N_CPMG_700.0': 500000000.0, '1H_CPMG_67.0': 500000000.0, '15N_CPMG_400.0': 500000000.0, '15N_CPMG_250.0': 500000000.0, '1H_CPMG_2133.0': 500000000.0, '1H_CPMG_1600.0': 500000000.0, '15N_CPMG_200.0': 500000000.0, '15N_CPMG_1000.0': 500000000.0, '15N_CPMG_500.0': 500000000.0, '15N_CPMG_600.0': 500000000.0}], 
6464              ['spectrometer_frq_count', 1], 
6465              ['spectrometer_frq_list', [500000000.0]], 
6466              ['spectrum_ids', ['1H_CPMG_67.0', '1H_CPMG_133.0', '1H_CPMG_267.0', '1H_CPMG_400.0', '1H_CPMG_533.0', '1H_CPMG_667.0', '1H_CPMG_800.0', '1H_CPMG_933.0', '1H_CPMG_1067.0', '1H_CPMG_1600.0', '1H_CPMG_2133.0', '1H_CPMG_2667.0', '15N_CPMG_50.0', '15N_CPMG_100.0', '15N_CPMG_150.0', '15N_CPMG_200.0', '15N_CPMG_250.0', '15N_CPMG_300.0', '15N_CPMG_350.0', '15N_CPMG_400.0', '15N_CPMG_500.0', '15N_CPMG_600.0', '15N_CPMG_700.0', '15N_CPMG_800.0', '15N_CPMG_900.0', '15N_CPMG_1000.0']] 
6467          ] 
6468          for name, value in data: 
6469              # Does it exist? 
6470              self.assert_(hasattr(cdp, name)) 
6471   
6472              # Check the object. 
6473              obj = getattr(cdp, name) 
6474              if not isinstance(data, dict): 
6475                  self.assertEqual(obj, value) 
6476   
6477              # Check the global dictionary data. 
6478              else: 
6479                  for id in ids: 
6480                      self.assertEqual(obj[id], value[id]) 
6481   
6482          # Check the spin data. 
6483          h_data = [ 
6484              [  67.0,  21.47924,   0.42958], 
6485              [ 133.0,  16.73898,   0.33478], 
6486              [ 267.0,   9.97357,   0.19947], 
6487              [ 400.0,   8.23877,   0.24737], 
6488              [ 533.0,   7.59290,   0.24263], 
6489              [ 667.0,   7.45843,   0.24165], 
6490              [ 800.0,   7.11222,   0.23915], 
6491              [ 933.0,   7.40880,   0.24129], 
6492              [1067.0,   6.55191,   0.16629], 
6493              [1600.0,   6.72177,   0.23637], 
6494              [2133.0,   7.09629,   0.23904], 
6495              [2667.0,   7.14675,   0.23940] 
6496          ] 
6497          for disp_point, value, error in h_data: 
6498              id = 'sq_cpmg_500.00000000_0.000_%.3f' % disp_point 
6499              self.assertEqual(cdp.mol[0].res[0].spin[0].r2eff[id], value) 
6500              self.assertEqual(cdp.mol[0].res[0].spin[0].r2eff_err[id], error) 
6501          n_data = [ 
6502              [  50.0,  27.15767,   0.54315], 
6503              [ 100.0,  26.55781,   0.53116], 
6504              [ 150.0,  24.73462,   0.49469], 
6505              [ 200.0,  20.98617,   0.41972], 
6506              [ 250.0,  17.82442,   0.35649], 
6507              [ 300.0,  15.55352,   0.31107], 
6508              [ 350.0,  13.78958,   0.27579], 
6509              [ 400.0,  12.48334,   0.24967], 
6510              [ 500.0,  11.55724,   0.23114], 
6511              [ 600.0,  10.53874,   0.21077], 
6512              [ 700.0,  10.07395,   0.20148], 
6513              [ 800.0,   9.62952,   0.19259], 
6514              [ 900.0,   9.49994,   0.19000], 
6515              [1000.0,   8.71350,   0.17427] 
6516          ] 
6517          for disp_point, value, error in n_data: 
6518              id = 'sq_cpmg_500.00000000_0.000_%.3f' % disp_point 
6519              self.assertEqual(cdp.mol[0].res[0].spin[1].r2eff[id], value) 
6520              self.assertEqual(cdp.mol[0].res[0].spin[1].r2eff_err[id], error) 
6521   
6522   
6523 -    def test_r2eff_fit_fixed_time(self): 
6524          """Test the relaxation dispersion 'R2eff' model for fixed time data in the auto-analysis.""" 
6525   
6526          # Execute the script. 
6527          self.interpreter.run(script_file=status.install_path + sep+'test_suite'+sep+'system_tests'+sep+'scripts'+sep+'relax_disp'+sep+'r2eff_calc.py') 
6528   
6529   
6530 -    def test_read_r2eff(self): 
6531          """Test the reading of a file containing r2eff values.""" 
6532   
6533          # Create the sequence data, and name the spins. 
6534          self.interpreter.residue.create(1, 'Gly') 
6535          self.interpreter.residue.create(2, 'Gly') 
6536          self.interpreter.residue.create(3, 'Gly') 
6537   
6538          # Read the file. 
6539          self.interpreter.relax_data.read(ri_id='R2eff.600', ri_type='R2eff', frq=600*1e6, file='r2eff.out', dir=status.install_path + sep+'test_suite'+sep+'shared_data'+sep+'dispersion'+sep+'r2eff', res_num_col=1, res_name_col=2, data_col=3, error_col=4) 
6540   
6541          # Test the data. 
6542          self.assertEqual(cdp.mol[0].res[0].spin[0].ri_data['R2eff.600'], 15.000) 
6543          self.assertEqual(cdp.mol[0].res[1].spin[0].ri_data['R2eff.600'], 4.2003) 
6544          self.assertEqual(cdp.mol[0].res[2].spin[0].ri_data['R2eff.600'], 7.2385) 
6545   
6546   
6547 -    def test_r20_from_min_r2eff_cpmg(self): 
6548          """Test speeding up grid search. Support requst sr #3151 U{https://gna.org/support/index.php?3151}. 
6549   
6550          User function to set the R20 parameters in the default grid search using the minimum R2eff value. 
6551   
6552          Optimisation of Kaare Teilum, Melanie H. Smith, Eike Schulz, Lea C. Christensen, Gleb Solomentseva, Mikael Oliveberg, and Mikael Akkea 2009 
6553          'SOD1-WT' CPMG data to the CR72 dispersion model. 
6554   
6555          This uses the data from paper at U{http://dx.doi.org/10.1073/pnas.0907387106}.  This is CPMG data with a fixed relaxation time period recorded at fields of 500 and 600MHz. 
6556          Data is for experiment at 25 degree Celcius. 
6557          """ 
6558   
6559          # Base data setup. 
6560          pipe_name = 'base pipe' 
6561          pipe_type = 'relax_disp' 
6562          pipe_name_r2eff = "%s_R2eff"%(pipe_name) 
6563          select_spin_index = list(range(0, 1)) 
6564          self.setup_sod1wt_t25(pipe_name=pipe_name, pipe_type=pipe_type, pipe_name_r2eff=pipe_name_r2eff, select_spin_index=select_spin_index) 
6565   
6566          # Generate r20 key. 
6567          r20_key_600 = generate_r20_key(exp_type=EXP_TYPE_CPMG_SQ, frq=599.8908617*1E6) 
6568          r20_key_500 = generate_r20_key(exp_type=EXP_TYPE_CPMG_SQ, frq=499.862139*1E6) 
6569   
6570          ## Now prepare for MODEL calculation. 
6571          MODEL = "CR72" 
6572   
6573          # Change pipe. 
6574          pipe_name_MODEL = "%s_%s"%(pipe_name, MODEL) 
6575          self.interpreter.pipe.copy(pipe_from=pipe_name_r2eff, pipe_to=pipe_name_MODEL) 
6576          self.interpreter.pipe.switch(pipe_name=pipe_name_MODEL) 
6577   
6578          # Then select model. 
6579          self.interpreter.relax_disp.select_model(model=MODEL) 
6580   
6581          # Set the R20 parameters in the default grid search using the minimum R2eff value. 
6582          self.interpreter.relax_disp.r20_from_min_r2eff(force=False) 
6583   
6584          # Test result, for normal run. 
6585          for spin, mol_name, resi, resn, spin_id in spin_loop(full_info=True, return_id=True, skip_desel=True): 
6586              # Get the spin_params. 
6587              spin_params = spin.params 
6588   
6589              # Defined fixed values for testing. 
6590              if spin_id == ":10@N": 
6591                  self.assertEqual(spin.r2[r20_key_600], 20.282732526087106) 
6592                  self.assertEqual(spin.r2[r20_key_500], 18.475299724356649) 
6593   
6594              # Print out. 
6595              print("r2_600=%2.2f r2_500=%2.2f spin_id=%s resi=%i resn=%s"%(spin.r2[r20_key_600], spin.r2[r20_key_500], spin_id, resi, resn)) 
6596   
6597              # Testing the r2 values for the different fields are not the same. 
6598              self.assert_(spin.r2[r20_key_600] != spin.r2[r20_key_500]) 
6599   
6600              # Test values are larger than 0. 
6601              self.assert_(spin.r2[r20_key_600] > 0.0) 
6602              self.assert_(spin.r2[r20_key_500] > 0.0) 
6603   
6604              # Loop over the experiment settings. 
6605              r2eff_600 = [] 
6606              r2eff_500 = [] 
6607              for exp_type, frq, offset, point, ei, mi, oi, di in loop_exp_frq_offset_point(return_indices=True): 
6608                  # Create the data key. 
6609                  data_key = return_param_key_from_data(exp_type=exp_type, frq=frq, offset=offset, point=point) 
6610   
6611                  # Extract the r2 eff data. 
6612                  r2eff = spin.r2eff[data_key] 
6613                  if frq == 599.8908617*1E6: 
6614                      r2eff_600.append(r2eff) 
6615                  elif frq == 499.862139*1E6: 
6616                      r2eff_500.append(r2eff) 
6617   
6618              # Sort values. 
6619              r2eff_600.sort() 
6620              r2eff_500.sort() 
6621   
6622              # Test values again. 
6623              print("For r20 600MHz min r2eff=%3.3f."%(min(r2eff_600))) 
6624              print(r2eff_600) 
6625              self.assertEqual(spin.r2[r20_key_600], min(r2eff_600)) 
6626              print("") 
6627   
6628              print("For r20 500MHz min r2eff=%3.3f."%(min(r2eff_500))) 
6629              print(r2eff_500) 
6630              self.assertEqual(spin.r2[r20_key_500], min(r2eff_500)) 
6631              print("") 
6632   
6633          print("###########################################") 
6634          print("Trying GRID SEARCH for minimum R2eff values") 
6635   
6636          ### Test just the Grid search. 
6637          GRID_INC = 5 
6638   
6639          self.interpreter.minimise.grid_search(lower=None, upper=None, inc=GRID_INC, constraints=True, verbosity=1) 
6640   
6641          ### Then test the value.set function. 
6642          # Change pipe. 
6643          pipe_name_MODEL = "%s_%s_2"%(pipe_name, MODEL) 
6644          self.interpreter.pipe.copy(pipe_from=pipe_name_r2eff, pipe_to=pipe_name_MODEL) 
6645          self.interpreter.pipe.switch(pipe_name=pipe_name_MODEL) 
6646   
6647          # Then select model. 
6648          self.interpreter.relax_disp.select_model(model=MODEL) 
6649   
6650          # Then set the standard parameter values. 
6651          for param in spin_params: 
6652              print("Setting standard parameter for param: %s"%param) 
6653              self.interpreter.value.set(param=param, index=None) 
6654   
6655          # Test result, for normal run. 
6656          for spin, mol_name, resi, resn, spin_id in spin_loop(full_info=True, return_id=True, skip_desel=True): 
6657              # Print out. 
6658              print("r2_600=%2.2f r2_500=%2.2f pA=%2.2f, dw=%2.2f, kex=%2.2f, spin_id=%s resi=%i resn=%s"%(spin.r2[r20_key_600], spin.r2[r20_key_500], spin.pA, spin.dw, spin.kex, spin_id, resi, resn)) 
6659   
6660              # Testing the r2 values. 
6661              self.assertEqual(spin.r2[r20_key_600], 10.00) 
6662              self.assertEqual(spin.r2[r20_key_500], 10.00) 
6663              self.assertEqual(spin.pA, 0.9) 
6664              self.assertEqual(spin.dw, 1.0) 
6665              self.assertEqual(spin.kex, 1000.0) 
6666   
6667          print("###########################################") 
6668          print("Trying GRID SEARCH for standard R2eff values") 
6669   
6670          ### Test just the Grid search. 
6671          GRID_INC = 5 
6672   
6673          self.interpreter.minimise.grid_search(lower=None, upper=None, inc=GRID_INC, constraints=True, verbosity=1) 
6674   
6675          ### Run auto_analysis. 
6676          # The grid search size (the number of increments per dimension). 
6677          GRID_INC = 5 
6678   
6679          # The number of Monte Carlo simulations to be used for error analysis at the end of the analysis. 
6680          MC_NUM = 3 
6681   
6682          # Model selection technique. 
6683          MODSEL = 'AIC' 
6684   
6685          # Execute the auto-analysis (fast). 
6686          # Standard parameters are: func_tol = 1e-25, grad_tol = None, max_iter = 10000000, 
6687          OPT_FUNC_TOL = 1e-1 
6688          relax_disp.Relax_disp.opt_func_tol = OPT_FUNC_TOL 
6689          OPT_MAX_ITERATIONS = 1000 
6690          relax_disp.Relax_disp.opt_max_iterations = OPT_MAX_ITERATIONS 
6691   
6692          # Run the analysis. 
6693          relax_disp.Relax_disp(pipe_name=pipe_name_r2eff, results_dir=ds.tmpdir, models=[MODEL], grid_inc=GRID_INC, mc_sim_num=MC_NUM, modsel=MODSEL, set_grid_r20=True) 
6694   
6695   
6696 -    def test_sod1wt_t25_bug_21954_order_error_analysis(self): 
6697          """Error analysis of SOD1-WT CPMG. From paper at U{http://dx.doi.org/10.1073/pnas.0907387106}. 
6698   
6699          Optimisation of Kaare Teilum, Melanie H. Smith, Eike Schulz, Lea C. Christensen, Gleb Solomentseva, Mikael Oliveberg, and Mikael Akkea 2009 
6700          'SOD1-WT' CPMG data to the CR72 dispersion model. 
6701   
6702          This uses the data from paper at U{http://dx.doi.org/10.1073/pnas.0907387106}.  This is CPMG data with a fixed relaxation time period recorded at fields of 500 and 600MHz. 
6703          Data is for experiment at 25 degree Celcius. 
6704   
6705          bug #21954 U{https://gna.org/bugs/index.php?21954}: Order of spectrum.error_analysis is important. 
6706          """ 
6707   
6708          # Base data setup. 
6709          pipe_name = 'base pipe' 
6710          pipe_type = 'relax_disp' 
6711          pipe_name_r2eff = "%s_R2eff"%(pipe_name) 
6712          select_spin_index = list(range(0, 1)) 
6713          self.setup_sod1wt_t25(pipe_name=pipe_name, pipe_type=pipe_type, pipe_name_r2eff=pipe_name_r2eff, select_spin_index=select_spin_index) 
6714   
6715          # Define replicated 
6716          repl_A = ['Z_A1', 'Z_A15'] 
6717          repl_B = ['Z_B1', 'Z_B18'] 
6718   
6719          # Loop over spectrum ID, and sort them 
6720          spectrum_ids_A = [] 
6721          spectrum_ids_B = [] 
6722          for spectrum_id in cdp.spectrum_ids: 
6723              if "A" in spectrum_id: 
6724                  spectrum_ids_A.append(spectrum_id) 
6725              elif "B" in spectrum_id: 
6726                  spectrum_ids_B.append(spectrum_id) 
6727   
6728          # To clean up old error analysis, delete attributes 
6729          delattr(cdp, "var_I") 
6730          delattr(cdp, "sigma_I") 
6731   
6732          # Perform error analysis 
6733          self.interpreter.spectrum.error_analysis(subset=spectrum_ids_A) 
6734          self.interpreter.spectrum.error_analysis(subset=spectrum_ids_B) 
6735   
6736          # Loop over spins, save errors to list 
6737          Errors_A_B = [] 
6738          for spin, mol_name, resi, resn, spin_id in spin_loop(full_info=True, return_id=True, skip_desel=True): 
6739              A_err = spin.peak_intensity_err[spectrum_ids_A[0]] 
6740              B_err = spin.peak_intensity_err[spectrum_ids_B[0]] 
6741              Errors_A_B.append([A_err, B_err]) 
6742   
6743          # To clean up old error analysis, delete attributes 
6744          delattr(cdp, "var_I") 
6745          delattr(cdp, "sigma_I") 
6746   
6747          # Perform error analysis. Order is important 
6748          self.interpreter.spectrum.error_analysis(subset=spectrum_ids_B) 
6749          self.interpreter.spectrum.error_analysis(subset=spectrum_ids_A) 
6750   
6751          # Loop over spins, save errors to list 
6752          Errors_B_A = [] 
6753          for spin, mol_name, resi, resn, spin_id in spin_loop(full_info=True, return_id=True, skip_desel=True): 
6754              A_err = spin.peak_intensity_err[spectrum_ids_A[0]] 
6755              B_err = spin.peak_intensity_err[spectrum_ids_B[0]] 
6756              Errors_B_A.append([A_err, B_err]) 
6757   
6758          # Make test for order of error 
6759          for i in range(len(Errors_A_B)): 
6760              Error_A_B = Errors_A_B[i] 
6761              Error_B_A = Errors_B_A[i] 
6762              self.assertAlmostEqual(Error_A_B[0], Error_B_A[0], 4) 
6763              self.assertAlmostEqual(Error_A_B[1], Error_B_A[1], 4) 
6764   
6765          # Make further tests for fixed values 
6766          std_A = math.sqrt((cdp.var_I[repl_A[0]] + cdp.var_I[repl_A[1]])/2) 
6767          std_A_fix = 2785.7263335738567 
6768   
6769          for id_A in spectrum_ids_A: 
6770              self.assertEqual(cdp.sigma_I[id_A], std_A) 
6771              self.assertAlmostEqual(cdp.sigma_I[id_A], std_A_fix, 7) 
6772   
6773          std_B = math.sqrt((cdp.var_I[repl_B[0]] + cdp.var_I[repl_B[1]])/2) 
6774          std_B_fix = 4967.3772030667988 
6775   
6776          for id_B in spectrum_ids_B: 
6777              self.assertEqual(cdp.sigma_I[id_B], std_B) 
6778              self.assertAlmostEqual(cdp.sigma_I[id_B], std_B_fix, 7) 
6779   
6780   
6781 -    def test_sod1wt_t25_to_cr72(self): 
6782          """Optimisation of SOD1-WT CPMG. From paper at U{http://dx.doi.org/10.1073/pnas.0907387106}. 
6783   
6784          Optimisation of Kaare Teilum, Melanie H. Smith, Eike Schulz, Lea C. Christensen, Gleb Solomentseva, Mikael Oliveberg, and Mikael Akkea 2009 
6785          'SOD1-WT' CPMG data to the CR72 dispersion model. 
6786   
6787          This uses the data from paper at U{http://dx.doi.org/10.1073/pnas.0907387106}.  This is CPMG data with a fixed relaxation time period recorded at fields of 500 and 600MHz. 
6788          Data is for experiment at 25 degree Celcius. 
6789          """ 
6790   
6791          # Base data setup. 
6792          pipe_name = 'base pipe' 
6793          pipe_type = 'relax_disp' 
6794          pipe_name_r2eff = "%s_R2eff"%(pipe_name) 
6795          select_spin_index = list(range(0, 2)) 
6796          self.setup_sod1wt_t25(pipe_name=pipe_name, pipe_type=pipe_type, pipe_name_r2eff=pipe_name_r2eff, select_spin_index=select_spin_index) 
6797   
6798          # Generate r20 key. 
6799          r20_key_600 = generate_r20_key(exp_type=EXP_TYPE_CPMG_SQ, frq=599.8908617*1E6) 
6800          r20_key_500 = generate_r20_key(exp_type=EXP_TYPE_CPMG_SQ, frq=499.862139*1E6) 
6801   
6802          ## Now prepare for MODEL calculation. 
6803          MODEL = "CR72" 
6804   
6805          # Change pipe. 
6806          pipe_name_MODEL = "%s_%s"%(pipe_name, MODEL) 
6807          self.interpreter.pipe.copy(pipe_from=pipe_name_r2eff, pipe_to=pipe_name_MODEL) 
6808          self.interpreter.pipe.switch(pipe_name=pipe_name_MODEL) 
6809   
6810          # Then select model. 
6811          self.interpreter.relax_disp.select_model(model=MODEL) 
6812   
6813          # GRID inc of 7 was found to be appropriate not to find pA = 0.5. 
6814          GRID_INC = 7 
6815   
6816          # Store grid and minimisations results. 
6817          grid_results = [] 
6818          mini_results = [] 
6819          clust_results = [] 
6820   
6821          # Set the R20 parameters in the default grid search using the minimum R2eff value. 
6822          self.interpreter.relax_disp.r20_from_min_r2eff(force=False) 
6823   
6824          # Deselect insignificant spins. 
6825          self.interpreter.relax_disp.insignificance(level=1.0) 
6826   
6827          # Perform Grid Search. 
6828          self.interpreter.minimise.grid_search(lower=None, upper=None, inc=GRID_INC, constraints=True, verbosity=1) 
6829   
6830          # Store result. 
6831          for spin, mol_name, resi, resn, spin_id in spin_loop(full_info=True, return_id=True, skip_desel=True): 
6832              # Store grid results. 
6833              grid_results.append([spin.r2[r20_key_600], spin.r2[r20_key_500], spin.dw, spin.pA, spin.kex, spin.chi2, spin_id, resi, resn]) 
6834   
6835          ## Now do minimisation. 
6836          # Standard parameters are: func_tol = 1e-25, grad_tol = None, max_iter = 10000000, 
6837          set_func_tol = 1e-9 
6838          set_max_iter = 100000 
6839          self.interpreter.minimise.execute(min_algor='simplex', func_tol=set_func_tol, max_iter=set_max_iter, constraints=True, scaling=True, verbosity=1) 
6840   
6841          # Store result. 
6842          pA_values = [] 
6843          kex_values = [] 
6844          for spin, mol_name, resi, resn, spin_id in spin_loop(full_info=True, return_id=True, skip_desel=True): 
6845              # Store minimisation results. 
6846              mini_results.append([spin.r2[r20_key_600], spin.r2[r20_key_500], spin.dw, spin.pA, spin.kex, spin.chi2, spin_id, resi, resn]) 
6847   
6848              # Store pA values. 
6849              pA_values.append(spin.pA) 
6850   
6851              # Store kex values. 
6852              kex_values.append(spin.kex) 
6853   
6854          print("\n# Now print before and after minimisation.\n") 
6855   
6856          # Print results. 
6857          for i in range(len(grid_results)): 
6858              # Get values. 
6859              g_r2_600, g_r2_500, g_dw, g_pA, g_kex, g_chi2, g_spin_id, g_resi, g_resn = grid_results[i] 
6860              m_r2_600, m_r2_500, m_dw, m_pA, m_kex, m_chi2, m_spin_id, m_resi, m_resn = mini_results[i] 
6861   
6862              print("GRID r2600=%2.2f r2500=%2.2f dw=%1.1f pA=%1.3f kex=%3.2f chi2=%3.2f spin_id=%s resi=%i resn=%s"%(g_r2_600, g_r2_500, g_dw, g_pA, g_kex, g_chi2, g_spin_id, g_resi, g_resn)) 
6863              print("MIN  r2600=%2.2f r2500=%2.2f dw=%1.1f pA=%1.3f kex=%3.2f chi2=%3.2f spin_id=%s resi=%i resn=%s"%(m_r2_600, m_r2_500, m_dw, m_pA, m_kex, m_chi2, m_spin_id, m_resi, m_resn)) 
6864   
6865          ## Prepare for clustering 
6866          # Change pipe. 
6867          pipe_name_MODEL_CLUSTER = "%s_%s_Cluster"%(pipe_name, MODEL) 
6868          self.interpreter.pipe.copy(pipe_from=pipe_name_r2eff, pipe_to=pipe_name_MODEL_CLUSTER) 
6869          self.interpreter.pipe.switch(pipe_name=pipe_name_MODEL_CLUSTER) 
6870   
6871          # Then select model. 
6872          self.interpreter.relax_disp.select_model(model=MODEL) 
6873   
6874          # Define cluster id. 
6875          cluster_id = 'clust' 
6876   
6877          # Loop over spins to cluster them. 
6878          for spin, mol_name, resi, resn, spin_id in spin_loop(full_info=True, return_id=True, skip_desel=True): 
6879              self.interpreter.relax_disp.cluster(cluster_id, spin_id) 
6880   
6881          # Copy over values. 
6882          self.interpreter.relax_disp.parameter_copy(pipe_from=pipe_name_MODEL, pipe_to=pipe_name_MODEL_CLUSTER) 
6883   
6884          # Test the median values is correct 
6885          for spin, mol_name, resi, resn, spin_id in spin_loop(full_info=True, return_id=True, skip_desel=True): 
6886              print(pA_values) 
6887              # The the median pA value returned. 
6888              self.assertEqual(median(pA_values), spin.pA) 
6889   
6890              # The the median kex value returned. 
6891              self.assertEqual(median(kex_values), spin.kex) 
6892   
6893          ## Now do minimisation. 
6894          self.interpreter.minimise.execute(min_algor='simplex', func_tol=set_func_tol, max_iter=set_max_iter, constraints=True, scaling=True, verbosity=1) 
6895   
6896          # Store result. 
6897          for spin, mol_name, resi, resn, spin_id in spin_loop(full_info=True, return_id=True, skip_desel=True): 
6898              # Store clust results. 
6899              clust_results.append([spin.r2[r20_key_600], spin.r2[r20_key_500], spin.dw, spin.pA, spin.kex, spin.chi2, spin_id, resi, resn]) 
6900   
6901              # Store the outcome of the clustering minimisation. 
6902              clust_pA = spin.pA 
6903              clust_kex = spin.kex 
6904   
6905          print("\n# Now testing.\n") 
6906   
6907          # Define results 
6908          test_res = {} 
6909          test_res[':10@N'] = {} 
6910          test_res[':10@N']['r2600'] = 18.429755324773360 
6911          test_res[':10@N']['r2500'] = 16.981349161968630 
6912          test_res[':10@N']['dw'] = 2.700755859433969 
6913          test_res[':10@N']['pA'] = 0.971531659288657 
6914          test_res[':10@N']['kex'] = 3831.766337047963134 
6915          test_res[':11@N'] = {} 
6916          test_res[':11@N']['r2600'] = 18.193409421115213 
6917          test_res[':11@N']['r2500'] = 17.308838135567765 
6918          test_res[':11@N']['dw'] = 2.706650302761793 
6919          test_res[':11@N']['pA'] = 0.971531659288657 
6920          test_res[':11@N']['kex'] = 3831.766337047963134 
6921   
6922          # Then make tests. 
6923          for i in range(len(grid_results)): 
6924              # Get values. 
6925              g_r2_600, g_r2_500, g_dw, g_pA, g_kex, g_chi2, g_spin_id, g_resi, g_resn = grid_results[i] 
6926              m_r2_600, m_r2_500, m_dw, m_pA, m_kex, m_chi2, m_spin_id, m_resi, m_resn = mini_results[i] 
6927              c_r2_600, c_r2_500, c_dw, c_pA, c_kex, c_chi2, c_spin_id, c_resi, c_resn = clust_results[i] 
6928   
6929              print("%s GRID   r2600=%2.2f r2500=%2.2f dw=%1.1f pA=%1.3f kex=%3.2f chi2=%3.2f spin_id=%s resi=%i resn=%s"%(g_spin_id, g_r2_600, g_r2_500, g_dw, g_pA, g_kex, g_chi2, g_spin_id, g_resi, g_resn)) 
6930              print("%s MIN    r2600=%2.2f r2500=%2.2f dw=%1.1f pA=%1.3f kex=%3.2f chi2=%3.2f spin_id=%s resi=%i resn=%s"%(m_spin_id, m_r2_600, m_r2_500, m_dw, m_pA, m_kex, m_chi2, m_spin_id, m_resi, m_resn)) 
6931              print("%s Clust  r2600=%2.2f r2500=%2.2f dw=%1.1f pA=%1.3f kex=%3.2f chi2=%3.2f spin_id=%s resi=%i resn=%s"%(m_spin_id, c_r2_600, c_r2_500, c_dw, c_pA, c_kex, c_chi2, c_spin_id, c_resi, c_resn)) 
6932   
6933              # Make tests. 
6934              self.assertEqual(clust_pA, c_pA) 
6935              self.assertEqual(clust_kex, c_kex) 
6936   
6937              # Test values. 
6938              if c_spin_id in test_res: 
6939                  self.assertAlmostEqual(c_r2_600, test_res[c_spin_id]['r2600'], 4) 
6940                  self.assertAlmostEqual(c_r2_500, test_res[c_spin_id]['r2500'], 4) 
6941                  self.assertAlmostEqual(c_dw, test_res[c_spin_id]['dw'], 3) 
6942                  self.assertAlmostEqual(c_pA, test_res[c_spin_id]['pA'], 5) 
6943                  self.assertAlmostEqual(c_kex, test_res[c_spin_id]['kex'], 1) 
6944   
6945          # Save disp graph to temp. 
6946          #self.interpreter.relax_disp.plot_disp_curves(dir="~"+sep+"test", num_points=1000, extend=500.0, force=True). 
6947   
6948   
6949 -    def test_sod1wt_t25_to_sherekhan_input(self): 
6950          """Conversion of SOD1-WT CPMG R2eff values into input files for sherekhan. 
6951   
6952          Optimisation of Kaare Teilum, Melanie H. Smith, Eike Schulz, Lea C. Christensen, Gleb Solomentseva, Mikael Oliveberg, and Mikael Akkea 2009 
6953          'SOD1-WT' CPMG data to the CR72 dispersion model. 
6954   
6955          This uses the data from paper at U{http://dx.doi.org/10.1073/pnas.0907387106}.  This is CPMG data with a fixed relaxation time period recorded at fields of 500 and 600MHz. 
6956          Data is for experiment at 25 degree Celcius. 
6957          """ 
6958   
6959          # Base data setup. 
6960          pipe_name = 'base pipe' 
6961          pipe_type = 'relax_disp' 
6962          pipe_name_r2eff = "%s_R2eff"%(pipe_name) 
6963          select_spin_index = list(range(0, 2)) 
6964          self.setup_sod1wt_t25(pipe_name=pipe_name, pipe_type=pipe_type, pipe_name_r2eff=pipe_name_r2eff, select_spin_index=select_spin_index) 
6965   
6966          # Generate r20 key. 
6967          r20_key_600 = generate_r20_key(exp_type=EXP_TYPE_CPMG_SQ, frq=599.8908617*1E6) 
6968          r20_key_500 = generate_r20_key(exp_type=EXP_TYPE_CPMG_SQ, frq=499.862139*1E6) 
6969   
6970          # Cluster everything, to analyse together. 
6971          self.interpreter.relax_disp.cluster(cluster_id='all', spin_id=":1-1000") 
6972   
6973          # Write input 
6974          self.interpreter.relax_disp.sherekhan_input(force=True, spin_id=None, dir=ds.tmpdir) 
6975   
6976          # Check the r2eff set files. 
6977          print("\nChecking the R2eff input set files.") 
6978          files = [[ds.tmpdir + sep + 'cluster1', 'sherekhan_frq1.in'], [ ds.tmpdir + sep + 'cluster1', 'sherekhan_frq2.in']] 
6979   
6980          # First check file exists 
6981          for dir, file in files: 
6982              print(dir+sep+file) 
6983              self.assert_(access(dir+sep+file, F_OK)) 
6984   
6985          # Define how files should look like 
6986          data_set_600 = [ 
6987               "60.8272464287\n", 
6988               "0.06\n", 
6989               "# nu_cpmg (Hz)       R2eff (rad/s)        Error               \n", 
6990               "# G10\n", 
6991               "              33.333       26.53556078711      0.5236104771163\n", 
6992               "              66.667       25.29735243318        0.48766574122\n", 
6993               "                 100       25.09470361403      0.4820438864671\n", 
6994               "             133.333       25.15603274331      0.4837377286085\n", 
6995               "             166.667       24.27213341753      0.4599457904395\n", 
6996               "                 200       24.00364120328      0.4529773198905\n", 
6997               "             266.667       24.03511395168      0.4537880662536\n", 
6998               "                 300       23.04761040024      0.4291039120557\n", 
6999               "             333.333       22.95530300787      0.4268745963972\n", 
7000               "                 400       23.06158810662      0.4294426293624\n", 
7001               "             466.667       22.26799054092      0.4106809618644\n", 
7002               "             533.333       21.99851418823      0.4045232104735\n", 
7003               "             666.667       21.19651570955      0.3868136173831\n", 
7004               "             833.333       20.30938498379      0.3682604887899\n", 
7005               "                1000       20.28273252609       0.367719392568\n", 
7006               "# D11\n", 
7007               "              33.333       24.76520269878      0.5026475808706\n", 
7008               "              66.667        24.8773107448      0.5058752916906\n", 
7009               "                 100       24.90357815239      0.5066348551479\n", 
7010               "             133.333        23.7782506151      0.4751950583865\n", 
7011               "             166.667       23.68548762076      0.4727017128631\n", 
7012               "                 200       23.58629651618      0.4700517377679\n", 
7013               "             266.667       23.47734671187      0.4671601744044\n", 
7014               "                 300       24.08647493772      0.4835855560598\n", 
7015               "             333.333       22.98314371029      0.4542918950801\n", 
7016               "                 400       22.80339361568      0.4497107885587\n", 
7017               "             466.667       22.91634335366      0.4525833037874\n", 
7018               "             533.333       22.59774140046      0.4445334311324\n", 
7019               "             666.667        20.9177750759      0.4046955726046\n", 
7020               "             833.333       20.71792550566      0.4002363835007\n", 
7021               "                1000       19.54080006349      0.3751112751853\n", 
7022          ] 
7023   
7024          # Check data_set_600 
7025          file = open(files[0][0]+sep+files[0][1]) 
7026          lines = file.readlines() 
7027          file.close() 
7028          self.assertEqual(len(data_set_600), len(lines)) 
7029          for i in range(len(data_set_600)): 
7030              # Make the string test 
7031              self.assertEqual(data_set_600[i], lines[i]) 
7032   
7033          # Define how files should look like 
7034          data_set_500 = [ 
7035               "50.6846152368\n", 
7036               "0.04\n", 
7037               "# nu_cpmg (Hz)       R2eff (rad/s)        Error               \n", 
7038               "# G10\n", 
7039               "                  50       22.28084307393      0.2944966344183\n", 
7040               "                 100       21.93494977761      0.2910362768307\n", 
7041               "                 150       21.09850032232       0.282892238351\n", 
7042               "                 200       20.86493960397      0.2806737853646\n", 
7043               "                 250       20.75287269752      0.2796178205016\n", 
7044               "                 300       20.25597152406      0.2750013546989\n", 
7045               "                 350       19.92172163467      0.2719555756504\n", 
7046               "                 400       19.97712052922       0.272457105051\n", 
7047               "                 450       19.46807010415      0.2678972122793\n", 
7048               "                 500       19.76875460947      0.2705774849203\n", 
7049               "                 550       19.39161367402      0.2672216964327\n", 
7050               "                 600       19.03949517697      0.2641417899694\n", 
7051               "                 650       19.12218812132      0.2648605059901\n", 
7052               "                 700       19.01037461457      0.2638893584683\n", 
7053               "                 800       18.83395162904      0.2623674321143\n", 
7054               "                 900       18.47529972436      0.2593123604687\n", 
7055               "                1000        18.5252023121      0.2597343394038\n", 
7056               "# D11\n", 
7057               "                  50       22.15403890237      0.3285588379827\n", 
7058               "                 100       21.80946781746      0.3247185598713\n", 
7059               "                 150       21.77715415505       0.324361526682\n", 
7060               "                 200       21.41647464235      0.3204122024881\n", 
7061               "                 250       21.17099940822      0.3177616325958\n", 
7062               "                 300       21.03740030577      0.3163316496664\n", 
7063               "                 350       20.95393648281      0.3154427665172\n", 
7064               "                 400       20.93311399332       0.315221543436\n", 
7065               "                 450       20.18219905222      0.3073848655291\n", 
7066               "                 500       19.93599065085      0.3048744697057\n", 
7067               "                 550       19.68475725452      0.3023424499113\n", 
7068               "                 600       19.33575433934      0.2988741928798\n", 
7069               "                 650       19.53915692194      0.3008886196853\n", 
7070               "                 700        19.2018754351      0.2975587767134\n", 
7071               "                 800       18.82360965368      0.2938866923878\n", 
7072               "                 900       18.71861761238      0.2928790380131\n", 
7073               "                1000       17.95878049287      0.2857341721151\n", 
7074          ] 
7075   
7076          # Check data_set_500 
7077          file = open(files[1][0]+sep+files[1][1]) 
7078          lines = file.readlines() 
7079          file.close() 
7080          self.assertEqual(len(data_set_500), len(lines)) 
7081          for i in range(len(data_set_500)): 
7082              # Make the string test 
7083              self.assertEqual(data_set_500[i], lines[i]) 
7084   
7085          # Test local dir tests. This will be turned off in system test. 
7086          turn_on_local_dir_test = False 
7087   
7088          if turn_on_local_dir_test: 
7089              ## Now check to local folder with None argument. 
7090              # Write input 
7091              self.interpreter.relax_disp.sherekhan_input(force=True, spin_id=None) 
7092   
7093              # Check the r2eff set files. 
7094              print("\nChecking the R2eff input set files.") 
7095              files = [[path.join(getcwd(), 'cluster1'), 'sherekhan_frq1.in'], [path.join(getcwd(), 'cluster1'), 'sherekhan_frq2.in']] 
7096   
7097              # First check file exists 
7098              for dir, file in files: 
7099                  print(dir+sep+file) 
7100                  self.assert_(access(dir+sep+file, F_OK)) 
7101   
7102              ## Now check to local folder with dir argument. 
7103              # Write input 
7104              set_dir = "Test_ShereKhan" 
7105              self.interpreter.relax_disp.sherekhan_input(force=True, spin_id=None, dir=set_dir) 
7106   
7107              # Check the r2eff set files. 
7108              print("\nChecking the R2eff input set files.") 
7109              files = [[path.join(getcwd(), set_dir, 'cluster1'), 'sherekhan_frq1.in'], [path.join(getcwd(), set_dir, 'cluster1'), 'sherekhan_frq2.in']] 
7110   
7111              # First check file exists 
7112              for dir, file in files: 
7113                  print(dir+sep+file) 
7114                  self.assert_(access(dir+sep+file, F_OK)) 
7115   
7116   
7117 -    def test_sprangers_data_to_mmq_cr72(self, model=None): 
7118          """Test the 'MMQ CR72' model fitting against Remco Sprangers' ClpP data. 
7119   
7120          This uses the data from Remco Sprangers' paper at http://dx.doi.org/10.1073/pnas.0507370102.  This is MMQ CPMG data with a fixed relaxation time period. 
7121          """ 
7122   
7123          # Reset. 
7124          self.interpreter.reset() 
7125   
7126          # Create the data pipe and load the base data. 
7127          data_path = status.install_path + sep+'test_suite'+sep+'shared_data'+sep+'dispersion'+sep+'Sprangers_ClpP' 
7128          self.interpreter.state.load(data_path+sep+'r2eff_values') 
7129   
7130          # The model data pipe. 
7131          model = 'MMQ CR72' 
7132          pipe_name = "%s - relax_disp" % model 
7133          self.interpreter.pipe.copy(pipe_from='base pipe', pipe_to=pipe_name, bundle_to='relax_disp') 
7134          self.interpreter.pipe.switch(pipe_name=pipe_name) 
7135   
7136          # Set the model. 
7137          self.interpreter.relax_disp.select_model(model=model) 
7138   
7139          # Cluster everything. 
7140          self.interpreter.relax_disp.cluster(cluster_id='all', spin_id=":135-137") 
7141   
7142          # Copy the data. 
7143          self.interpreter.value.copy(pipe_from='R2eff', pipe_to=pipe_name, param='r2eff') 
7144   
7145          # Alias the spins. 
7146          spin135S = cdp.mol[0].res[0].spin[0] 
7147          spin135F = cdp.mol[0].res[0].spin[1] 
7148          spin137S = cdp.mol[0].res[1].spin[0] 
7149          spin137F = cdp.mol[0].res[1].spin[1] 
7150   
7151          # The R20 keys. 
7152          r20_key1 = generate_r20_key(exp_type=EXP_TYPE_CPMG_MQ, frq=600e6) 
7153          r20_key2 = generate_r20_key(exp_type=EXP_TYPE_CPMG_MQ, frq=800e6) 
7154   
7155          # Set the cluster specific parameters (only for the first spin). 
7156          spin135S.pA = 0.836591763632 
7157          spin135S.kex = 241.806525261 
7158   
7159          # Set the initial parameter values. 
7160          spin135S.r2 = {r20_key1: 28.2493431552, r20_key2: 31.7517334715} 
7161          spin135S.dw = 0.583003118785 
7162          spin135S.dwH = 0.0361441944301 
7163   
7164          spin135F.r2 = {r20_key1: 42.7201839991, r20_key2: 57.3178617389} 
7165          spin135F.dw = 0.805849745104 
7166          spin135F.dwH = 0.0215791945715 
7167   
7168          spin137S.r2 = {r20_key1: 26.0134115256, r20_key2: 30.575806934} 
7169          spin137S.dw = 0.688107568372 
7170          spin137S.dwH = 0.0344463604043 
7171   
7172          spin137F.r2 = {r20_key1: 46.6969397337, r20_key2: 58.602384101} 
7173          spin137F.dw = 0.94978299907 
7174          spin137F.dwH = 1.4818877939e-07 
7175   
7176          # Low precision optimisation. 
7177          self.interpreter.minimise.execute(min_algor='simplex', func_tol=1e-10, max_iter=1000) 
7178   
7179          # Printout. 
7180          print("\n\nOptimised parameters:\n") 
7181          print("%-20s %-20s %-20s %-20s %-20s" % ("Parameter", "Value (:135@S)", "Value (:135@F)", "Value (:137@S)", "Value (:137@F)")) 
7182          print("%-20s %20.15g %20.15g %20.15g %20.15g" % ("R2 (500 MHz)", spin135S.r2[r20_key1], spin135F.r2[r20_key1], spin137S.r2[r20_key1], spin137F.r2[r20_key1])) 
7183          print("%-20s %20.15g %20.15g %20.15g %20.15g" % ("R2 (800 MHz)", spin135S.r2[r20_key2], spin135F.r2[r20_key2], spin137S.r2[r20_key2], spin137F.r2[r20_key2])) 
7184          print("%-20s %20.15g %20.15g %20.15g %20.15g" % ("pA", spin135S.pA, spin135F.pA, spin137S.pA, spin137F.pA)) 
7185          print("%-20s %20.15g %20.15g %20.15g %20.15g" % ("dw", spin135S.dw, spin135F.dw, spin137S.dw, spin137F.dw)) 
7186          print("%-20s %20.15g %20.15g %20.15g %20.15g" % ("dwH", spin135S.dwH, spin135F.dwH, spin137S.dwH, spin137F.dwH)) 
7187          print("%-20s %20.15g %20.15g %20.15g %20.15g" % ("kex", spin135S.kex, spin135F.kex, spin137S.kex, spin137F.kex)) 
7188          print("%-20s %20.15g %20.15g %20.15g %20.15g\n" % ("chi2", spin135S.chi2, spin135F.chi2, spin137S.chi2, spin137F.chi2)) 
7189          print("\n        # Set the cluster specific parameters (only for the first spin).") 
7190          print("        spin135S.pA = %s" % spin135S.pA) 
7191          print("        spin135S.kex = %s" % spin135S.kex) 
7192          print("\n        # Set the initial parameter values.") 
7193          print("        spin135S.r2 = {r20_key1: %s, r20_key2: %s}" % (spin135S.r2[r20_key1], spin135S.r2[r20_key2])) 
7194          print("        spin135S.dw = %s" % spin135S.dw) 
7195          print("        spin135S.dwH = %s" % spin135S.dwH) 
7196          print("\n        spin135F.r2 = {r20_key1: %s, r20_key2: %s}" % (spin135F.r2[r20_key1], spin135F.r2[r20_key2])) 
7197          print("        spin135F.dw = %s" % spin135F.dw) 
7198          print("        spin135F.dwH = %s" % spin135F.dwH) 
7199          print("\n        spin137S.r2 = {r20_key1: %s, r20_key2: %s}" % (spin137S.r2[r20_key1], spin137S.r2[r20_key2])) 
7200          print("        spin137S.dw = %s" % spin137S.dw) 
7201          print("        spin137S.dwH = %s" % spin137S.dwH) 
7202          print("\n        spin137F.r2 = {r20_key1: %s, r20_key2: %s}" % (spin137F.r2[r20_key1], spin137F.r2[r20_key2])) 
7203          print("        spin137F.dw = %s" % spin137F.dw) 
7204          print("        spin137F.dwH = %s" % spin137F.dwH) 
7205   
7206          # Checks for residue :135S. 
7207          self.assertAlmostEqual(spin135S.r2[r20_key1], 28.2493445347425, 4) 
7208          self.assertAlmostEqual(spin135S.r2[r20_key2], 31.7517352342937, 4) 
7209          self.assertAlmostEqual(spin135S.pA, 0.836591714049569, 4) 
7210          self.assertAlmostEqual(spin135S.dw, 0.583003004605869, 4) 
7211          self.assertAlmostEqual(spin135S.dwH, 0.0361441894065963, 4) 
7212          self.assertAlmostEqual(spin135S.kex/100, 241.806464344233/100, 4) 
7213          self.assertAlmostEqual(spin135S.chi2, 12.4224060116473, 4) 
7214   
7215          # Checks for residue :135F. 
7216          self.assertAlmostEqual(spin135F.r2[r20_key1], 42.7201844426839, 4) 
7217          self.assertAlmostEqual(spin135F.r2[r20_key2], 57.3178718548898, 4) 
7218          self.assertAlmostEqual(spin135F.pA, 0.836591714049569, 4) 
7219          self.assertAlmostEqual(spin135F.dw, 0.805849748711916, 4) 
7220          self.assertAlmostEqual(spin135F.dwH, 0.0215791669142752, 4) 
7221          self.assertAlmostEqual(spin135F.kex/100, 241.806464344233/100, 4) 
7222          self.assertAlmostEqual(spin135F.chi2, 12.4224060116473, 4) 
7223   
7224          # Checks for residue :137S. 
7225          self.assertAlmostEqual(spin137S.r2[r20_key1], 26.013412509919, 4) 
7226          self.assertAlmostEqual(spin137S.r2[r20_key2], 30.5758092335097, 4) 
7227          self.assertAlmostEqual(spin137S.pA, 0.836591714049569, 4) 
7228          self.assertAlmostEqual(spin137S.dw, 0.688107406812537, 4) 
7229          self.assertAlmostEqual(spin137S.dwH, 0.034446357344577, 4) 
7230          self.assertAlmostEqual(spin137S.kex/100, 241.806464344233/100, 4) 
7231          self.assertAlmostEqual(spin137S.chi2, 12.4224060116473, 4) 
7232   
7233          # Checks for residue :137F. 
7234          self.assertAlmostEqual(spin137F.r2[r20_key1], 46.696935090697, 4) 
7235          self.assertAlmostEqual(spin137F.r2[r20_key2], 58.6023842513446, 4) 
7236          self.assertAlmostEqual(spin137F.pA, 0.836591714049569, 4) 
7237          self.assertAlmostEqual(spin137F.dw, 0.94978325541294, 4) 
7238          self.assertAlmostEqual(spin137F.dwH, 1.5189362257653e-07, 4) 
7239          self.assertAlmostEqual(spin137F.kex/100, 241.806464344233/100, 4) 
7240          self.assertAlmostEqual(spin137F.chi2, 12.4224060116473, 4) 
7241   
7242   
7243 -    def test_sprangers_data_to_ns_mmq_2site(self, model=None): 
7244          """Test the 'NS MMQ 2-site' model fitting against Remco Sprangers' ClpP data. 
7245   
7246          This uses the data from Remco Sprangers' paper at http://dx.doi.org/10.1073/pnas.0507370102.  This is MQ CPMG data with a fixed relaxation time period. 
7247          """ 
7248   
7249          # Reset. 
7250          self.interpreter.reset() 
7251   
7252          # Create the data pipe and load the base data. 
7253          data_path = status.install_path + sep+'test_suite'+sep+'shared_data'+sep+'dispersion'+sep+'Sprangers_ClpP' 
7254          self.interpreter.state.load(data_path+sep+'r2eff_values') 
7255   
7256          # The model data pipe. 
7257          model = 'NS MMQ 2-site' 
7258          pipe_name = "%s - relax_disp" % model 
7259          self.interpreter.pipe.copy(pipe_from='base pipe', pipe_to=pipe_name, bundle_to='relax_disp') 
7260          self.interpreter.pipe.switch(pipe_name=pipe_name) 
7261   
7262          # Set the model. 
7263          self.interpreter.relax_disp.select_model(model=model) 
7264   
7265          # Cluster everything. 
7266          self.interpreter.relax_disp.cluster(cluster_id='all', spin_id=":135-137") 
7267   
7268          # Copy the data. 
7269          self.interpreter.value.copy(pipe_from='R2eff', pipe_to=pipe_name, param='r2eff') 
7270   
7271          # Alias the spins. 
7272          spin135S = cdp.mol[0].res[0].spin[0] 
7273          spin135F = cdp.mol[0].res[0].spin[1] 
7274          spin137S = cdp.mol[0].res[1].spin[0] 
7275          spin137F = cdp.mol[0].res[1].spin[1] 
7276   
7277          # The R20 keys. 
7278          r20_key1 = generate_r20_key(exp_type=EXP_TYPE_CPMG_MQ, frq=800e6) 
7279          r20_key2 = generate_r20_key(exp_type=EXP_TYPE_CPMG_MQ, frq=800e6) 
7280   
7281          # Set the cluster specific parameters (only for the first spin). 
7282          spin135S.pA = 0.847378444499757 
7283          spin135S.kex = 264.055604934724329 
7284   
7285          # Set the initial parameter values. 
7286          spin135S.r2 = {r20_key1: 30.315119723745390, r20_key2: 37.411874745645299} 
7287          spin135S.dw = 0.585574008745351 
7288          spin135S.dwH = 0.000000000000002 
7289   
7290          spin135F.r2 = {r20_key1: 41.440843383778287, r20_key2: 56.989726795397893} 
7291          spin135F.dw = 0.856699277665748 
7292          spin135F.dwH = 0.000000000582587 
7293   
7294          spin137S.r2 = {r20_key1: 23.051695938570266, r20_key2: 28.352806483953824} 
7295          spin137S.dw = 0.772904450844973 
7296          spin137S.dwH = 0.183351478512970 
7297   
7298          spin137F.r2 = {r20_key1: 44.702032074210429, r20_key2: 56.453146052685319} 
7299          spin137F.dw = 0.984568590342831 
7300          spin137F.dwH = 0.000000001993458 
7301   
7302          # Low precision optimisation. 
7303          self.interpreter.minimise.execute(min_algor='simplex', line_search=None, hessian_mod=None, hessian_type=None, func_tol=1e-5, grad_tol=None, max_iter=100, constraints=True, scaling=True, verbosity=1) 
7304   
7305          # Printout. 
7306          print("\n\nOptimised parameters:\n") 
7307          print("%-20s %-20s %-20s %-20s %-20s" % ("Parameter", "Value (:135@S)", "Value (:135@F)", "Value (:137@S)", "Value (:137@F)")) 
7308          print("%-20s %20.15g %20.15g %20.15g %20.15g" % ("R2 (500 MHz)", spin135S.r2[r20_key1], spin135F.r2[r20_key1], spin137S.r2[r20_key1], spin137F.r2[r20_key1])) 
7309          print("%-20s %20.15g %20.15g %20.15g %20.15g" % ("R2 (800 MHz)", spin135S.r2[r20_key2], spin135F.r2[r20_key2], spin137S.r2[r20_key2], spin137F.r2[r20_key2])) 
7310          print("%-20s %20.15g %20.15g %20.15g %20.15g" % ("pA", spin135S.pA, spin135F.pA, spin137S.pA, spin137F.pA)) 
7311          print("%-20s %20.15g %20.15g %20.15g %20.15g" % ("dw", spin135S.dw, spin135F.dw, spin137S.dw, spin137F.dw)) 
7312          print("%-20s %20.15g %20.15g %20.15g %20.15g" % ("dwH", spin135S.dwH, spin135F.dwH, spin137S.dwH, spin137F.dwH)) 
7313          print("%-20s %20.15g %20.15g %20.15g %20.15g" % ("kex", spin135S.kex, spin135F.kex, spin137S.kex, spin137F.kex)) 
7314          print("%-20s %20.15g %20.15g %20.15g %20.15g\n" % ("chi2", spin135S.chi2, spin135F.chi2, spin137S.chi2, spin137F.chi2)) 
7315   
7316          # FIXME: Remove this temporary return and properly check the results. 
7317          return 
7318   
7319          # Checks for residue :135S. 
7320          self.assertAlmostEqual(spin135S.r2[r20_key1], 30.3151197237454, 4) 
7321          self.assertAlmostEqual(spin135S.r2[r20_key2], 37.4118747456453, 4) 
7322          self.assertAlmostEqual(spin135S.pA, 0.847378444499757, 4) 
7323          self.assertAlmostEqual(spin135S.dw, 0.585574008745351, 4) 
7324          self.assertAlmostEqual(spin135S.dwH, 2e-15, 4) 
7325          self.assertAlmostEqual(spin135S.kex, 264.055604934724, 4) 
7326          self.assertAlmostEqual(spin135S.chi2, 13.859423588071, 1) 
7327   
7328          # Checks for residue :135F. 
7329          self.assertAlmostEqual(spin135F.r2[r20_key1], 41.4408433837783, 4) 
7330          self.assertAlmostEqual(spin135F.r2[r20_key2], 56.9897267953979, 4) 
7331          self.assertAlmostEqual(spin135F.pA, 0.847378444499757, 4) 
7332          self.assertAlmostEqual(spin135F.dw, 0.856699277665748, 4) 
7333          self.assertAlmostEqual(spin135F.dwH, 5.82587e-10, 4) 
7334          self.assertAlmostEqual(spin135F.kex, 264.055604934724, 4) 
7335          self.assertAlmostEqual(spin135F.chi2, 13.859423588071, 1) 
7336   
7337          # Checks for residue :137S. 
7338          self.assertAlmostEqual(spin137S.r2[r20_key1], 23.0516959385703, 4) 
7339          self.assertAlmostEqual(spin137S.r2[r20_key2], 28.3528064839538, 4) 
7340          self.assertAlmostEqual(spin137S.pA, 0.847378444499757, 4) 
7341          self.assertAlmostEqual(spin137S.dw, 0.772904450844973, 4) 
7342          self.assertAlmostEqual(spin137S.dwH, 0.18335147851297, 4) 
7343          self.assertAlmostEqual(spin137S.kex, 264.055604934724, 4) 
7344          self.assertAlmostEqual(spin137S.chi2, 13.859423588071, 1) 
7345   
7346          # Checks for residue :137F. 
7347          self.assertAlmostEqual(spin137F.r2[r20_key1], 44.7020320742104, 4) 
7348          self.assertAlmostEqual(spin137F.r2[r20_key2], 56.4531460526853, 4) 
7349          self.assertAlmostEqual(spin137F.pA, 0.847378444499757, 4) 
7350          self.assertAlmostEqual(spin137F.dw, 0.984568590342831, 4) 
7351          self.assertAlmostEqual(spin137F.dwH, 2.0931309e-09, 4) 
7352          self.assertAlmostEqual(spin137F.kex, 264.055604934724, 4) 
7353          self.assertAlmostEqual(spin137F.chi2, 13.859423588071, 1) 
7354   
7355   
7356 -    def test_tp02_data_to_ns_r1rho_2site(self, model=None): 
7357          """Test the relaxation dispersion 'NS R1rho 2-site' model fitting against the 'TP02' test data.""" 
7358   
7359          # Setup the data. 
7360          self.setup_tp02_data_to_ns_r1rho_2site() 
7361   
7362          # Alias the spins. 
7363          spin1 = cdp.mol[0].res[0].spin[0] 
7364          spin2 = cdp.mol[0].res[1].spin[0] 
7365   
7366          # The R20 keys. 
7367          r20_key1 = generate_r20_key(exp_type=EXP_TYPE_R1RHO, frq=500e6) 
7368          r20_key2 = generate_r20_key(exp_type=EXP_TYPE_R1RHO, frq=800e6) 
7369   
7370          # Checks for residue :1. 
7371          self.assertAlmostEqual(spin1.r2[r20_key1], 8.50207717367548, 4) 
7372          self.assertAlmostEqual(spin1.r2[r20_key2], 13.4680429589972, 4) 
7373          self.assertAlmostEqual(spin1.pA, 0.864523128842393, 4) 
7374          self.assertAlmostEqual(spin1.dw, 8.85204828994151, 4) 
7375          self.assertAlmostEqual(spin1.kex/1000, 1199.56359549637/1000, 4) 
7376          self.assertAlmostEqual(spin1.chi2, 2.99182130153514, 4) 
7377   
7378          # Checks for residue :2. 
7379          self.assertAlmostEqual(spin2.r2[r20_key1], 10.2099357790203, 4) 
7380          self.assertAlmostEqual(spin2.r2[r20_key2], 16.2137648697873, 4) 
7381          self.assertAlmostEqual(spin2.pA, 0.836488681031685, 4) 
7382          self.assertAlmostEqual(spin2.dw, 9.5505714779503, 4) 
7383          self.assertAlmostEqual(spin2.kex/1000, 1454.45726998929/1000, 4) 
7384          self.assertAlmostEqual(spin2.chi2, 0.000402231563481261, 4) 
7385   
7386   
7387 -    def test_tp02_data_to_ns_r1rho_2site_cluster(self, model=None): 
7388          """Test the relaxation dispersion 'NS R1rho 2-site' model fitting against the 'TP02' test data, when performing clustering.""" 
7389   
7390          # Setup the data. 
7391          self.setup_tp02_data_to_ns_r1rho_2site(clustering=True) 
7392   
7393          # Alias the spins. 
7394          spin1 = cdp.mol[0].res[0].spin[0] 
7395          spin2 = cdp.mol[0].res[1].spin[0] 
7396   
7397          # The R20 keys. 
7398          r20_key1 = generate_r20_key(exp_type=EXP_TYPE_R1RHO, frq=500e6) 
7399          r20_key2 = generate_r20_key(exp_type=EXP_TYPE_R1RHO, frq=800e6) 
7400   
7401          # Checks for residue :1. 
7402          self.assertAlmostEqual(spin1.r2[r20_key1], 8.48607207881462, 4) 
7403          self.assertAlmostEqual(spin1.r2[r20_key2], 13.4527609061722, 4) 
7404          self.assertAlmostEqual(spin1.pA, 0.863093838784425, 4) 
7405          self.assertAlmostEqual(spin1.dw, 8.86218096536618, 4) 
7406          self.assertAlmostEqual(spin1.kex/1000, 1186.22749648299/1000, 4) 
7407          self.assertAlmostEqual(spin1.chi2, 3.09500996065247, 4) 
7408   
7409          # Checks for residue :2. 
7410          self.assertAlmostEqual(spin2.r2[r20_key1], 10.4577906018883, 4) 
7411          self.assertAlmostEqual(spin2.r2[r20_key2], 16.4455550953792, 4) 
7412          self.assertAlmostEqual(spin2.pA, 0.863093838784425, 4) 
7413          self.assertAlmostEqual(spin2.dw, 11.5841168862587, 4) 
7414          self.assertAlmostEqual(spin2.kex/1000, 1186.22749648299/1000, 4) 
7415          self.assertAlmostEqual(spin2.chi2, 3.09500996065247, 4) 
7416   
7417   
7418 -    def test_tp02_data_to_mp05(self): 
7419          """Test the dispersion 'MP05' model fitting against the 'TP02' test data.""" 
7420   
7421          # Fixed time variable and the models. 
7422          ds.fixed = True 
7423          ds.models = ['R2eff', 'MP05'] 
7424   
7425          # Execute the script. 
7426          self.interpreter.run(script_file=status.install_path + sep+'test_suite'+sep+'system_tests'+sep+'scripts'+sep+'relax_disp'+sep+'r1rho_off_res_tp02.py') 
7427   
7428          # Switch back to the data pipe for the optimisation. 
7429          self.interpreter.pipe.switch('MP05 - relax_disp') 
7430   
7431          # The equivalent MP05 parameters. 
7432          r1rho_prime = [[10.0058086343329, 15.005806870124], [12.0766320470785, 18.0767503536277]] 
7433          pA = [0.775055484521586, 0.500000000036595] 
7434          kex = [1235.20361276079, 2378.31403454691] 
7435          delta_omega = [7.08194146569694, 5.4083562844306] 
7436          chi2 = [0.0370400968727768, 0.182141732163934] 
7437   
7438          # Alias the spins. 
7439          spin1 = cdp.mol[0].res[0].spin[0] 
7440          spin2 = cdp.mol[0].res[1].spin[0] 
7441   
7442          # The R20 keys. 
7443          r20_key1 = generate_r20_key(exp_type=EXP_TYPE_R1RHO, frq=500e6) 
7444          r20_key2 = generate_r20_key(exp_type=EXP_TYPE_R1RHO, frq=800e6) 
7445   
7446          # Printout. 
7447          print("\n\nOptimised parameters:\n") 
7448          print("%-20s %-20s %-20s" % ("Parameter", "Value (:1)", "Value (:2)")) 
7449          print("%-20s %20.15g %20.15g" % ("R2 (500 MHz)", spin1.r2[r20_key1], spin2.r2[r20_key1])) 
7450          print("%-20s %20.15g %20.15g" % ("R2 (800 MHz)", spin1.r2[r20_key2], spin2.r2[r20_key2])) 
7451          print("%-20s %20.15g %20.15g" % ("pA", spin1.pA, spin2.pA)) 
7452          print("%-20s %20.15g %20.15g" % ("dw", spin1.dw, spin2.dw)) 
7453          print("%-20s %20.15g %20.15g" % ("kex", spin1.kex, spin2.kex)) 
7454          print("%-20s %20.15g %20.15g\n" % ("chi2", spin1.chi2, spin2.chi2)) 
7455   
7456          # Check each spin. 
7457          spin_index = 0 
7458          for spin, spin_id in spin_loop(return_id=True): 
7459              # Printout. 
7460              print("\nSpin %s." % spin_id) 
7461   
7462              # Check the fitted parameters. 
7463              self.assertAlmostEqual(spin.r2[r20_key1]/10, r1rho_prime[spin_index][0]/10, 4) 
7464              self.assertAlmostEqual(spin.r2[r20_key2]/10, r1rho_prime[spin_index][1]/10, 4) 
7465              self.assertAlmostEqual(spin.pA, pA[spin_index], 3) 
7466              self.assertAlmostEqual(spin.dw, delta_omega[spin_index], 3) 
7467              self.assertAlmostEqual(spin.kex/1000.0, kex[spin_index]/1000.0, 3) 
7468              self.assertAlmostEqual(spin.chi2, chi2[spin_index], 3) 
7469   
7470              # Increment the spin index. 
7471              spin_index += 1 
7472   
7473   
7474 -    def test_tp02_data_to_tap03(self): 
7475          """Test the dispersion 'TAP03' model fitting against the 'TP02' test data.""" 
7476   
7477          # Fixed time variable and the models. 
7478          ds.fixed = True 
7479          ds.models = ['R2eff', 'TAP03'] 
7480   
7481          # Execute the script. 
7482          self.interpreter.run(script_file=status.install_path + sep+'test_suite'+sep+'system_tests'+sep+'scripts'+sep+'relax_disp'+sep+'r1rho_off_res_tp02.py') 
7483   
7484          # Switch back to the data pipe for the optimisation. 
7485          self.interpreter.pipe.switch('TAP03 - relax_disp') 
7486   
7487          # The equivalent TAP03 parameters. 
7488          r1rho_prime = [[10.0058156589442, 15.005818505006], [12.0766046472748, 18.076648462452]] 
7489          pA = [0.775042569092891, 0.500000000229685] 
7490          kex = [1235.20852748765, 2379.47085580169] 
7491          delta_omega = [7.08176806468445, 5.40708372863538] 
7492          chi2 = [0.0371366837083293, 0.182212857256044] 
7493   
7494          # Alias the spins. 
7495          spin1 = cdp.mol[0].res[0].spin[0] 
7496          spin2 = cdp.mol[0].res[1].spin[0] 
7497   
7498          # The R20 keys. 
7499          r20_key1 = generate_r20_key(exp_type=EXP_TYPE_R1RHO, frq=500e6) 
7500          r20_key2 = generate_r20_key(exp_type=EXP_TYPE_R1RHO, frq=800e6) 
7501   
7502          # Printout. 
7503          print("\n\nOptimised parameters:\n") 
7504          print("%-20s %-20s %-20s" % ("Parameter", "Value (:1)", "Value (:2)")) 
7505          print("%-20s %20.15g %20.15g" % ("R2 (500 MHz)", spin1.r2[r20_key1], spin2.r2[r20_key1])) 
7506          print("%-20s %20.15g %20.15g" % ("R2 (800 MHz)", spin1.r2[r20_key2], spin2.r2[r20_key2])) 
7507          print("%-20s %20.15g %20.15g" % ("pA", spin1.pA, spin2.pA)) 
7508          print("%-20s %20.15g %20.15g" % ("dw", spin1.dw, spin2.dw)) 
7509          print("%-20s %20.15g %20.15g" % ("kex", spin1.kex, spin2.kex)) 
7510          print("%-20s %20.15g %20.15g\n" % ("chi2", spin1.chi2, spin2.chi2)) 
7511   
7512          # Switch to the 'MP05' model data pipe, then check for each spin. 
7513          self.interpreter.pipe.switch('TAP03 - relax_disp') 
7514          spin_index = 0 
7515          for spin, spin_id in spin_loop(return_id=True): 
7516              # Printout. 
7517              print("\nSpin %s." % spin_id) 
7518   
7519              # Check the fitted parameters. 
7520              self.assertAlmostEqual(spin.r2[r20_key1]/10, r1rho_prime[spin_index][0]/10, 4) 
7521              self.assertAlmostEqual(spin.r2[r20_key2]/10, r1rho_prime[spin_index][1]/10, 4) 
7522              self.assertAlmostEqual(spin.pA, pA[spin_index], 3) 
7523              self.assertAlmostEqual(spin.dw, delta_omega[spin_index], 3) 
7524              self.assertAlmostEqual(spin.kex/1000.0, kex[spin_index]/1000.0, 3) 
7525              self.assertAlmostEqual(spin.chi2, chi2[spin_index], 3) 
7526   
7527              # Increment the spin index. 
7528              spin_index += 1 
7529   
7530   
7531 -    def test_tp02_data_to_tp02(self): 
7532          """Test the relaxation dispersion 'TP02' model curve fitting to fixed time synthetic data.""" 
7533   
7534          # Fixed time variable. 
7535          ds.fixed = True 
7536   
7537          # Execute the script. 
7538          self.interpreter.run(script_file=status.install_path + sep+'test_suite'+sep+'system_tests'+sep+'scripts'+sep+'relax_disp'+sep+'r1rho_off_res_tp02.py') 
7539   
7540          # The original parameters. 
7541          r1rho_prime = [[10.0, 15.0], [12.0, 18.0]] 
7542          pA = 0.7654321 
7543          kex = 1234.56789 
7544          delta_omega = [7.0, 9.0] 
7545   
7546          # The R20 keys. 
7547          r20_key1 = generate_r20_key(exp_type=EXP_TYPE_R1RHO, frq=500e6) 
7548          r20_key2 = generate_r20_key(exp_type=EXP_TYPE_R1RHO, frq=800e6) 
7549   
7550          # Switch to the 'TP02' model data pipe, then check for each spin. 
7551          self.interpreter.pipe.switch('TP02 - relax_disp') 
7552          spin_index = 0 
7553          for spin, spin_id in spin_loop(return_id=True): 
7554              # Printout. 
7555              print("\nSpin %s." % spin_id) 
7556   
7557              # Check the fitted parameters. 
7558              self.assertAlmostEqual(spin.r2[r20_key1]/10, r1rho_prime[spin_index][0]/10, 4) 
7559              self.assertAlmostEqual(spin.r2[r20_key2]/10, r1rho_prime[spin_index][1]/10, 4) 
7560              self.assertAlmostEqual(spin.dw, delta_omega[spin_index], 3) 
7561              self.assertAlmostEqual(spin.kex/1000.0, kex/1000.0, 3) 
7562   
7563              # Increment the spin index. 
7564              spin_index += 1 
7565   
7566   
7567 -    def test_value_write_calc_rotating_frame_params_int(self): 
7568          """System test of the value.write function to write intensities for an R1rho setup. 
7569          This system test is to make sure, that modifying the API for special parameters theta and w_eff does not alter the functionality value.write. 
7570   
7571          This uses the data of the saved state attached to U{bug #21344<https://gna.org/bugs/?21344>}. 
7572          """ 
7573   
7574          # Load the state. 
7575          statefile = status.install_path+sep+'test_suite'+sep+'shared_data'+sep+'dispersion'+sep+'bug_21344_trunc.bz2' 
7576          self.interpreter.state.load(statefile, force=True) 
7577   
7578          # Set filepaths. 
7579          int_filepath = ds.tmpdir+sep+'int.out' 
7580   
7581          # Write out the intensity parameter file. 
7582          # The writing out of intensity file is to make sure the API function retains its function after modification for special parameters. 
7583          self.interpreter.value.write(param='peak_intensity', file='int.out', dir=ds.tmpdir, scaling=1.0, force=True) 
7584   
7585          # Test the file exists. 
7586          self.assert_(access(int_filepath, F_OK)) 
7587   
7588          # Open the files for testing. 
7589          int_file = open(int_filepath, 'r') 
7590   
7591          # Loop over the intensity file to test values. 
7592          for line in int_file: 
7593              # Skip lines starting with #. 
7594              if line[0] == "#": 
7595                  continue 
7596   
7597              # Split the line 
7598              linesplit = line.split() 
7599   
7600              # Assume values 
7601              if linesplit[0] == "None" and linesplit[1] == "5" and linesplit[2] == "I": 
7602                  self.assertEqual(linesplit[5], "115571.4") 
7603              elif linesplit[0] == "None" and linesplit[1] == "6" and linesplit[2] == "S": 
7604                  self.assertEqual(linesplit[5], "68377.52") 
7605              elif linesplit[0] == "None" and linesplit[1] == "8" and linesplit[2] == "S": 
7606                  self.assertEqual(linesplit[5], "9141.689") 
7607              elif linesplit[0] == "None" and linesplit[1] == "9" and linesplit[2] == "A": 
7608                  self.assertEqual(linesplit[5], "29123.77") 
7609              elif linesplit[0] == "None" and linesplit[1] == "10" and linesplit[2] == "L": 
7610                  self.assertEqual(linesplit[5], "58914.94") 
7611   
7612          # Close files 
7613          int_file.close() 
7614   
7615   
7616 -    def test_value_write_calc_rotating_frame_params_theta(self): 
7617          """System test of the value.write function to write return values of theta from calc_rotating_frame_params() function for an R1rho setup. 
7618   
7619          This uses the data of the saved state attached to U{bug #21344<https://gna.org/bugs/?21344>}. 
7620          """ 
7621   
7622          # Load the state. 
7623          statefile = status.install_path+sep+'test_suite'+sep+'shared_data'+sep+'dispersion'+sep+'bug_21344_trunc.bz2' 
7624          self.interpreter.state.load(statefile, force=True) 
7625   
7626          # Set filepaths. 
7627          theta_filepath = ds.tmpdir+sep+'theta.out' 
7628   
7629          # Write out the theta parameter file. 
7630          self.interpreter.value.write(param='theta', file='theta.out', dir=ds.tmpdir, scaling=1.0, force=True) 
7631   
7632          # Test the file exists. 
7633          self.assert_(access(theta_filepath, F_OK)) 
7634   
7635          # Open the files for testing. 
7636          theta_file = open(theta_filepath, 'r') 
7637   
7638          # Loop over the theta file to test values. 
7639          for line in theta_file: 
7640              # Skip lines starting with #. 
7641              if line[0] == "#": 
7642                  continue 
7643              # Print lines, not including newline character. 
7644              print(line[:-1]) 
7645   
7646              # Split the line 
7647              linesplit = line.split() 
7648   
7649              # Assume values 
7650              if linesplit[0] == "None" and linesplit[1] == "5" and linesplit[2] == "I": 
7651                  self.assertNotEqual(linesplit[5], "None") 
7652              elif linesplit[0] == "None" and linesplit[1] == "6" and linesplit[2] == "S": 
7653                  self.assertNotEqual(linesplit[5], "None") 
7654              elif linesplit[0] == "None" and linesplit[1] == "8" and linesplit[2] == "S": 
7655                  self.assertNotEqual(linesplit[5], "None") 
7656              elif linesplit[0] == "None" and linesplit[1] == "9" and linesplit[2] == "A": 
7657                  self.assertNotEqual(linesplit[5], "None") 
7658              elif linesplit[0] == "None" and linesplit[1] == "10" and linesplit[2] == "L": 
7659                  self.assertNotEqual(linesplit[5], "None") 
7660   
7661          # Close files 
7662          theta_file.close() 
7663   
7664   
7665 -    def test_value_write_calc_rotating_frame_params_w_eff(self): 
7666          """System test of the value.write function to write return values of w_eff from calc_rotating_frame_params() function for an R1rho setup. 
7667   
7668          This uses the data of the saved state attached to U{bug #21344<https://gna.org/bugs/?21344>}. 
7669          """ 
7670   
7671          # Load the state. 
7672          statefile = status.install_path+sep+'test_suite'+sep+'shared_data'+sep+'dispersion'+sep+'bug_21344_trunc.bz2' 
7673          self.interpreter.state.load(statefile, force=True) 
7674   
7675          # Set filepaths. 
7676          w_eff_filepath = ds.tmpdir+sep+'w_eff.out' 
7677   
7678          # Write out the w_eff parameter file. 
7679          self.interpreter.value.write(param='w_eff', file='w_eff.out', dir=ds.tmpdir, scaling=1.0, force=True) 
7680   
7681          # Test the file exists. 
7682          self.assert_(access(w_eff_filepath, F_OK)) 
7683   
7684          # Open the files for testing. 
7685          w_eff_file = open(w_eff_filepath, 'r') 
7686   
7687          # Loop over the w_eff file to test values. 
7688          for line in w_eff_file: 
7689              # Skip lines starting with #. 
7690              if line[0] == "#": 
7691                  continue 
7692              # Print lines, not including newline character. 
7693              print(line[:-1]) 
7694   
7695              # Split the line 
7696              linesplit = line.split() 
7697   
7698              # Assume values 
7699              if linesplit[0] == "None" and linesplit[1] == "5" and linesplit[2] == "I": 
7700                  self.assertNotEqual(linesplit[5], "None") 
7701              elif linesplit[0] == "None" and linesplit[1] == "6" and linesplit[2] == "S": 
7702                  self.assertNotEqual(linesplit[5], "None") 
7703              elif linesplit[0] == "None" and linesplit[1] == "8" and linesplit[2] == "S": 
7704                  self.assertNotEqual(linesplit[5], "None") 
7705              elif linesplit[0] == "None" and linesplit[1] == "9" and linesplit[2] == "A": 
7706                  self.assertNotEqual(linesplit[5], "None") 
7707              elif linesplit[0] == "None" and linesplit[1] == "10" and linesplit[2] == "L": 
7708                  self.assertNotEqual(linesplit[5], "None") 
7709   
7710          # Close files 
7711          w_eff_file.close() 
7712   
7713   
7714 -    def test_value_write_calc_rotating_frame_params_auto_analysis(self): 
7715          """System test of the auto_analysis value.write function to write theta and w_eff values for an R1rho setup. 
7716   
7717          This uses the data of the saved state attached to U{bug #21344<https://gna.org/bugs/?21344>}. 
7718          """ 
7719   
7720          # Load the state. 
7721          statefile = status.install_path+sep+'test_suite'+sep+'shared_data'+sep+'dispersion'+sep+'bug_21344.bz2' 
7722          self.interpreter.state.load(statefile, force=True) 
7723   
7724          # Set pipe name, bundle and type. 
7725          pipe_name = 'base pipe' 
7726          pipe_bundle = 'relax_disp' 
7727          pipe_type = 'relax_disp' 
7728   
7729          # The path to the data files. 
7730          data_path = status.install_path + sep+'test_suite'+sep+'shared_data'+sep+'dispersion'+sep+'Kjaergaard_et_al_2013' 
7731   
7732          # Deselect all spins 
7733          self.interpreter.deselect.all() 
7734   
7735          # Specify spins to be selected. 
7736          select_spin_ids = [ 
7737          ":13@N", 
7738          ":15@N", 
7739          ":16@N", 
7740          ":25@N", 
7741          ":26@N", 
7742          ":28@N", 
7743          ":39@N", 
7744          ":40@N", 
7745          ":41@N", 
7746          ":43@N", 
7747          ":44@N", 
7748          ":45@N", 
7749          ":49@N", 
7750          ":52@N", 
7751          ":53@N"] 
7752   
7753          # Reverse the selection for the spins. 
7754          for curspin in select_spin_ids: 
7755              print("Selecting spin %s"%curspin) 
7756              self.interpreter.deselect.reverse(spin_id=curspin) 
7757   
7758          # Read the R1 data 
7759          self.interpreter.relax_data.read(ri_id='R1', ri_type='R1', frq=cdp.spectrometer_frq_list[0], file='R1_fitted_values.txt', dir=data_path, mol_name_col=1, res_num_col=2, res_name_col=3, spin_num_col=4, spin_name_col=5, data_col=6, error_col=7) 
7760   
7761          # The dispersion models. 
7762          MODELS = ['R2eff'] 
7763   
7764          # The grid search size (the number of increments per dimension). 
7765          GRID_INC = 4 
7766   
7767          # The number of Monte Carlo simulations to be used for error analysis at the end of the analysis. 
7768          MC_NUM = 3 
7769   
7770          # Model selection technique. 
7771          MODSEL = 'AIC' 
7772   
7773          # Execute the auto-analysis (fast). 
7774          # Standard parameters are: func_tol = 1e-25, grad_tol = None, max_iter = 10000000, 
7775          OPT_FUNC_TOL = 1e-1 
7776          relax_disp.Relax_disp.opt_func_tol = OPT_FUNC_TOL 
7777          OPT_MAX_ITERATIONS = 1000 
7778          relax_disp.Relax_disp.opt_max_iterations = OPT_MAX_ITERATIONS 
7779   
7780          # Run the analysis. 
7781          relax_disp.Relax_disp(pipe_name=pipe_name, pipe_bundle=pipe_bundle, results_dir=ds.tmpdir, models=MODELS, grid_inc=GRID_INC, mc_sim_num=MC_NUM, modsel=MODSEL) 
7782   
7783          ## Check for file creation 
7784          # Set filepaths. 
7785          theta_filepath = ds.tmpdir+sep+MODELS[0]+sep+'theta.out' 
7786          w_eff_filepath = ds.tmpdir+sep+MODELS[0]+sep+'w_eff.out' 
7787   
7788          # Test the files exists. 
7789          self.assert_(access(theta_filepath, F_OK)) 
7790          self.assert_(access(w_eff_filepath, F_OK)) 
7791   
7792          # Open the files for testing. 
7793          theta_file = open(theta_filepath, 'r') 
7794          theta_result = [ 
7795              "# Parameter description:  Rotating frame tilt angle : ( theta = arctan(w_1 / Omega) ) (rad).\n", 
7796              "#\n", 
7797              "# mol_name    res_num    res_name    spin_num    spin_name    r1rho_799.77739910_118.078_1341.110    sd(r1rho_799.77739910_118.078_1341.110)    r1rho_799.77739910_118.078_1648.500    sd(r1rho_799.77739910_118.078_1648.500)    r1rho_799.77739910_118.078_431.000    sd(r1rho_799.77739910_118.078_431.000)    r1rho_799.77739910_118.078_651.200    sd(r1rho_799.77739910_118.078_651.200)    r1rho_799.77739910_118.078_800.500    sd(r1rho_799.77739910_118.078_800.500)    r1rho_799.77739910_118.078_984.000    sd(r1rho_799.77739910_118.078_984.000)    r1rho_799.77739910_124.247_1341.110    sd(r1rho_799.77739910_124.247_1341.110)    r1rho_799.77739910_130.416_1341.110    sd(r1rho_799.77739910_130.416_1341.110)    r1rho_799.77739910_130.416_1648.500    sd(r1rho_799.77739910_130.416_1648.500)    r1rho_799.77739910_130.416_800.500    sd(r1rho_799.77739910_130.416_800.500)    r1rho_799.77739910_142.754_1341.110    sd(r1rho_799.77739910_142.754_1341.110)    r1rho_799.77739910_142.754_800.500    sd(r1rho_799.77739910_142.754_800.500)    r1rho_799.77739910_179.768_1341.110    sd(r1rho_799.77739910_179.768_1341.110)    r1rho_799.77739910_241.459_1341.110    sd(r1rho_799.77739910_241.459_1341.110)    \n", 
7798              "None          5          I           None        N            None                                   None                                       None                                   None                                       None                                  None                                      None                                  None                                      None                                  None                                      None                                  None                                      None                                   None                                       None                                   None                                       None                                   None                                       None                                  None                                      None                                   None                                       None                                  None                                      None                                   None                                       None                                   None                                       \n", 
7799              "None          6          S           None        N            None                                   None                                       None                                   None                                       None                                  None                                      None                                  None                                      None                                  None                                      None                                  None                                      None                                   None                                       None                                   None                                       None                                   None                                       None                                  None                                      None                                   None                                       None                                  None                                      None                                   None                                       None                                   None                                       \n", 
7800              "None          8          S           None        N            None                                   None                                       None                                   None                                       None                                  None                                      None                                  None                                      None                                  None                                      None                                  None                                      None                                   None                                       None                                   None                                       None                                   None                                       None                                  None                                      None                                   None                                       None                                  None                                      None                                   None                                       None                                   None                                       \n", 
7801              "None          9          A           None        N            None                                   None                                       None                                   None                                       None                                  None                                      None                                  None                                      None                                  None                                      None                                  None                                      None                                   None                                       None                                   None                                       None                                   None                                       None                                  None                                      None                                   None                                       None                                  None                                      None                                   None                                       None                                   None                                       \n", 
7802              "None          10         L           None        N            None                                   None                                       None                                   None                                       None                                  None                                      None                                  None                                      None                                  None                                      None                                  None                                      None                                   None                                       None                                   None                                       None                                   None                                       None                                  None                                      None                                   None                                       None                                  None                                      None                                   None                                       None                                   None                                       \n", 
7803              "None          11         Q           None        N            None                                   None                                       None                                   None                                       None                                  None                                      None                                  None                                      None                                  None                                      None                                  None                                      None                                   None                                       None                                   None                                       None                                   None                                       None                                  None                                      None                                   None                                       None                                  None                                      None                                   None                                       None                                   None                                       \n", 
7804              "None          12         D           None        N            None                                   None                                       None                                   None                                       None                                  None                                      None                                  None                                      None                                  None                                      None                                  None                                      None                                   None                                       None                                   None                                       None                                   None                                       None                                  None                                      None                                   None                                       None                                  None                                      None                                   None                                       None                                   None                                       \n", 
7805              "None          13         L           None        N                1.83827367612531                   None                                           1.79015307643158                   None                                            2.2768687598681                  None                                          2.08461171779445                  None                                          2.00120623474388                  None                                          1.92825070277699                  None                                          1.47212860033516                   None                                           1.12978017906854                   None                                           1.20415336139956                   None                                          0.901691390796334                  None                                         0.687390207543568                   None                                          0.455635480573046                  None                                         0.281637123971289                   None                                          0.138259661766539                   None                                       \n", 
7806              "None          14         L           None        N            None                                   None                                       None                                   None                                       None                                  None                                      None                                  None                                      None                                  None                                      None                                  None                                      None                                   None                                       None                                   None                                       None                                   None                                       None                                  None                                      None                                   None                                       None                                  None                                      None                                   None                                       None                                   None                                       \n", 
7807              "None          15         R           None        N                1.58367544790673                   None                                           1.58127411936947                   None                                           1.61085209029811                  None                                          1.59731540507347                  None                                          1.59237108385522                  None                                          1.58834866344307                  None                                           1.2251048782537                   None                                          0.938142786712004                   None                                           1.03297495592991                   None                                          0.683284686224254                  None                                         0.594447788256641                   None                                          0.383528609383686                  None                                         0.262780814059893                   None                                          0.133469839450564                   None                                       \n", 
7808              "None          16         T           None        N                1.40984232256624                   None                                           1.43947245672073                   None                                           1.10299856647417                  None                                          1.24811470332083                  None                                          1.30521602599932                  None                                          1.35302443831853                  None                                          1.07923777467974                   None                                          0.833345927788896                   None                                          0.934350308974616                   None                                          0.581325254389991                  None                                         0.543659670184793                   None                                          0.346238480454282                  None                                         0.251454336191817                   None                                          0.130436714663781                   None                                       \n", 
7809              "None          17         L           None        N            None                                   None                                       None                                   None                                       None                                  None                                      None                                  None                                      None                                  None                                      None                                  None                                      None                                   None                                       None                                   None                                       None                                   None                                       None                                  None                                      None                                   None                                       None                                  None                                      None                                   None                                       None                                   None                                       \n", 
7810              "None          18         K           None        N            None                                   None                                       None                                   None                                       None                                  None                                      None                                  None                                      None                                  None                                      None                                  None                                      None                                   None                                       None                                   None                                       None                                   None                                       None                                  None                                      None                                   None                                       None                                  None                                      None                                   None                                       None                                   None                                       \n", 
7811              "None          19         S           None        N            None                                   None                                       None                                   None                                       None                                  None                                      None                                  None                                      None                                  None                                      None                                  None                                      None                                   None                                       None                                   None                                       None                                   None                                       None                                  None                                      None                                   None                                       None                                  None                                      None                                   None                                       None                                   None                                       \n", 
7812              "None          21         S           None        N            None                                   None                                       None                                   None                                       None                                  None                                      None                                  None                                      None                                  None                                      None                                  None                                      None                                   None                                       None                                   None                                       None                                   None                                       None                                  None                                      None                                   None                                       None                                  None                                      None                                   None                                       None                                   None                                       \n", 
7813              "None          24         Q           None        N            None                                   None                                       None                                   None                                       None                                  None                                      None                                  None                                      None                                  None                                      None                                  None                                      None                                   None                                       None                                   None                                       None                                   None                                       None                                  None                                      None                                   None                                       None                                  None                                      None                                   None                                       None                                   None                                       \n", 
7814              "None          25         Q           None        N                1.81569700258844                   None                                           1.77137827615015                   None                                           2.23175875585624                  None                                          2.04612705363098                  None                                           1.9673155780155                  None                                          1.89908711012298                  None                                          1.44829660124856                   None                                           1.11023386429581                   None                                           1.18716091371256                   None                                          0.877306975624962                  None                                         0.677790118853413                   None                                          0.447932002242236                  None                                         0.279785379050945                   None                                          0.137802891887767                   None                                       \n", 
7815              "None          26         Q           None        N                1.61128821168674                   None                                           1.60374392042003                   None                                           1.69619923953765                  None                                          1.65403989292986                  None                                          1.63856717205868                  None                                          1.62595755714564                  None                                          1.24977859227795                   None                                          0.956353494917591                   None                                           1.04972090035774                   None                                          0.702164059520172                  None                                         0.603227813742091                   None                                          0.390116910781037                  None                                         0.264658552037535                   None                                          0.133960994297096                   None                                       \n", 
7816              "None          27         Q           None        N            None                                   None                                       None                                   None                                       None                                  None                                      None                                  None                                      None                                  None                                      None                                  None                                      None                                   None                                       None                                   None                                       None                                   None                                       None                                  None                                      None                                   None                                       None                                  None                                      None                                   None                                       None                                   None                                       \n", 
7817              "None          28         Q           None        N                1.65182797011356                   None                                           1.63676707684161                   None                                           1.81830827892972                  None                                           1.7365089711986                  None                                          1.70601955220877                  None                                          1.68102938663686                  None                                          1.28685736157369                   None                                          0.984047498595701                   None                                            1.0749792109454                   None                                          0.731585685663053                  None                                         0.616577997665602                   None                                          0.400219205533665                  None                                         0.267471993812649                   None                                          0.134690869499646                   None                                       \n", 
7818              "None          29         V           None        N            None                                   None                                       None                                   None                                       None                                  None                                      None                                  None                                      None                                  None                                      None                                  None                                      None                                   None                                       None                                   None                                       None                                   None                                       None                                  None                                      None                                   None                                       None                                  None                                      None                                   None                                       None                                   None                                       \n", 
7819              "None          30         L           None        N            None                                   None                                       None                                   None                                       None                                  None                                      None                                  None                                      None                                  None                                      None                                  None                                      None                                   None                                       None                                   None                                       None                                   None                                       None                                  None                                      None                                   None                                       None                                  None                                      None                                   None                                       None                                   None                                       \n", 
7820              "None          31         N           None        N            None                                   None                                       None                                   None                                       None                                  None                                      None                                  None                                      None                                  None                                      None                                  None                                      None                                   None                                       None                                   None                                       None                                   None                                       None                                  None                                      None                                   None                                       None                                  None                                      None                                   None                                       None                                   None                                       \n", 
7821              "None          32         I           None        N            None                                   None                                       None                                   None                                       None                                  None                                      None                                  None                                      None                                  None                                      None                                  None                                      None                                   None                                       None                                   None                                       None                                   None                                       None                                  None                                      None                                   None                                       None                                  None                                      None                                   None                                       None                                   None                                       \n", 
7822              "None          33         L           None        N            None                                   None                                       None                                   None                                       None                                  None                                      None                                  None                                      None                                  None                                      None                                  None                                      None                                   None                                       None                                   None                                       None                                   None                                       None                                  None                                      None                                   None                                       None                                  None                                      None                                   None                                       None                                   None                                       \n", 
7823              "None          34         K           None        N            None                                   None                                       None                                   None                                       None                                  None                                      None                                  None                                      None                                  None                                      None                                  None                                      None                                   None                                       None                                   None                                       None                                   None                                       None                                  None                                      None                                   None                                       None                                  None                                      None                                   None                                       None                                   None                                       \n", 
7824              "None          35         S           None        N            None                                   None                                       None                                   None                                       None                                  None                                      None                                  None                                      None                                  None                                      None                                  None                                      None                                   None                                       None                                   None                                       None                                   None                                       None                                  None                                      None                                   None                                       None                                  None                                      None                                   None                                       None                                   None                                       \n", 
7825              "None          36         N           None        N            None                                   None                                       None                                   None                                       None                                  None                                      None                                  None                                      None                                  None                                      None                                  None                                      None                                   None                                       None                                   None                                       None                                   None                                       None                                  None                                      None                                   None                                       None                                  None                                      None                                   None                                       None                                   None                                       \n", 
7826              "None          38         Q           None        N            None                                   None                                       None                                   None                                       None                                  None                                      None                                  None                                      None                                  None                                      None                                  None                                      None                                   None                                       None                                   None                                       None                                   None                                       None                                  None                                      None                                   None                                       None                                  None                                      None                                   None                                       None                                   None                                       \n", 
7827              "None          39         L           None        N                1.76426439181176                   None                                           1.72885318885161                   None                                           2.11826300085737                  None                                          1.95430201082222                  None                                          1.88794717058464                  None                                          1.83172922971397                  None                                          1.39549951193417                   None                                           1.06783946148624                   None                                           1.14997013232702                   None                                          0.826128785942585                  None                                         0.657105386950171                   None                                          0.431542911580536                  None                                         0.275725736430539                   None                                          0.136791385554619                   None                                       \n", 
7828              "None          40         M           None        N                 1.5521741199158                   None                                           1.55564594516135                   None                                           1.51290906497298                  None                                          1.53245929150759                  None                                          1.53960430408466                  None                                          1.54541832596591                  None                                          1.19750223001929                   None                                          0.917959090226757                   None                                           1.01428385962747                   None                                          0.662779584695967                  None                                         0.584708929219264                   None                                          0.376271266885303                  None                                         0.260671619214194                   None                                          0.132914250767089                   None                                       \n", 
7829              "None          41         A           None        N                1.68339451828261                   None                                           1.66252964414082                   None                                           1.90911961276946                  None                                          1.79959323497326                  None                                          1.75801925517113                  None                                          1.72370710837265                  None                                          1.31646868936419                   None                                           1.00647189763597                   None                                           1.09525348649914                   None                                           0.75605702767542                  None                                         0.627395557358039                   None                                          0.408481831044309                  None                                         0.269716174238842                   None                                          0.135267948387412                   None                                       \n", 
7830              "None          42         A           None        N            None                                   None                                       None                                   None                                       None                                  None                                      None                                  None                                      None                                  None                                      None                                  None                                      None                                   None                                       None                                   None                                       None                                   None                                       None                                  None                                      None                                   None                                       None                                  None                                      None                                   None                                       None                                   None                                       \n", 
7831              "None          43         F           None        N                1.58506597154432                   None                                           1.58240542750303                   None                                           1.61517196062351                  None                                          1.60017740004898                  None                                          1.59469990835425                  None                                          1.59024353162528                  None                                          1.22633651794829                   None                                          0.939047922181951                   None                                           1.03380990731605                   None                                          0.684214484755514                  None                                         0.594884298549546                   None                                          0.383855128702894                  None                                         0.262874695048502                   None                                           0.13349447283116                   None                                       \n", 
7832              "None          44         I           None        N                1.57575471961837                   None                                           1.57483015671791                   None                                           1.58622388390755                  None                                          1.58100758841935                  None                                          1.57910319967536                  None                                          1.57755415552211                  None                                          1.21811077066835                   None                                          0.933010299763027                   None                                           1.02823520295828                   None                                           0.67802911457195                  None                                         0.591972285081647                   None                                          0.381678892926696                  None                                         0.262247347241724                   None                                          0.133329708422379                   None                                       \n", 
7833              "None          45         K           None        N                1.77147501495754                   None                                           1.73479633022489                   None                                           2.13509660780385                  None                                          1.96751045408372                  None                                          1.89924480319914                  None                                          1.84124387452692                  None                                          1.40277881643715                   None                                           1.07361367582571                   None                                           1.15506365550891                   None                                          0.832963505534767                  None                                         0.659913187081268                   None                                          0.433751178249555                  None                                         0.276282572106685                   None                                           0.13693095791902                   None                                       \n", 
7834              "None          46         Q           None        N            None                                   None                                       None                                   None                                       None                                  None                                      None                                  None                                      None                                  None                                      None                                  None                                      None                                   None                                       None                                   None                                       None                                   None                                       None                                  None                                      None                                   None                                       None                                  None                                      None                                   None                                       None                                   None                                       \n", 
7835              "None          48         T           None        N            None                                   None                                       None                                   None                                       None                                  None                                      None                                  None                                      None                                  None                                      None                                  None                                      None                                   None                                       None                                   None                                       None                                   None                                       None                                  None                                      None                                   None                                       None                                  None                                      None                                   None                                       None                                   None                                       \n", 
7836              "None          49         A           None        N                2.00297059962685                   None                                           1.92978318052058                   None                                           2.53305709323468                  None                                          2.33052197276846                  None                                          2.22870514722639                  None                                          2.13201782446864                  None                                           1.6587904412969                   None                                           1.29333162369472                   None                                           1.34311052758116                   None                                           1.12559033900783                  None                                         0.770195063841652                   None                                          0.524846264860003                  None                                         0.296857751274362                   None                                          0.141908833673671                   None                                       \n", 
7837              "None          50         K           None        N            None                                   None                                       None                                   None                                       None                                  None                                      None                                  None                                      None                                  None                                      None                                  None                                      None                                   None                                       None                                   None                                       None                                   None                                       None                                  None                                      None                                   None                                       None                                  None                                      None                                   None                                       None                                   None                                       \n", 
7838              "None          51         Y           None        N            None                                   None                                       None                                   None                                       None                                  None                                      None                                  None                                      None                                  None                                      None                                  None                                      None                                   None                                       None                                   None                                       None                                   None                                       None                                  None                                      None                                   None                                       None                                  None                                      None                                   None                                       None                                   None                                       \n", 
7839              "None          52         V           None        N                1.82421571143794                   None                                           1.77845404105203                   None                                           2.24910726268822                  None                                          2.06078232916932                  None                                          1.98017451806059                  None                                          1.91012195713554                  None                                          1.45724107606646                   None                                           1.11753869321304                   None                                           1.19352234944057                   None                                          0.886361068343012                  None                                         0.681372607920812                   None                                          0.450799407357501                  None                                         0.280478735779163                   None                                          0.137974257665877                   None                                       \n", 
7840              "None          53         A           None        N                2.05019708195234                   None                                           1.97089957318506                   None                                           2.58789168363698                  None                                          2.39027806684801                  None                                          2.28731354878582                  None                                           2.1872118539319                  None                                           1.7165709935896                   None                                           1.34832362477229                   None                                           1.38879751095815                   None                                            1.2085314357749                  None                                         0.799450059125864                   None                                          0.550583841461621                  None                                          0.30195492609136                   None                                          0.143090604877102                   None                                       \n", 
7841              "None          54         N           None        N            None                                   None                                       None                                   None                                       None                                  None                                      None                                  None                                      None                                  None                                      None                                  None                                      None                                   None                                       None                                   None                                       None                                   None                                       None                                  None                                      None                                   None                                       None                                  None                                      None                                   None                                       None                                   None                                       \n", 
7842              "None          55         Q           None        N            None                                   None                                       None                                   None                                       None                                  None                                      None                                  None                                      None                                  None                                      None                                  None                                      None                                   None                                       None                                   None                                       None                                   None                                       None                                  None                                      None                                   None                                       None                                  None                                      None                                   None                                       None                                   None                                       \n", 
7843              "None          57         G           None        N            None                                   None                                       None                                   None                                       None                                  None                                      None                                  None                                      None                                  None                                      None                                  None                                      None                                   None                                       None                                   None                                       None                                   None                                       None                                  None                                      None                                   None                                       None                                  None                                      None                                   None                                       None                                   None                                       \n", 
7844              "None          58         M           None        N            None                                   None                                       None                                   None                                       None                                  None                                      None                                  None                                      None                                  None                                      None                                  None                                      None                                   None                                       None                                   None                                       None                                   None                                       None                                  None                                      None                                   None                                       None                                  None                                      None                                   None                                       None                                   None                                       \n", 
7845              "None          59         Q           None        N            None                                   None                                       None                                   None                                       None                                  None                                      None                                  None                                      None                                  None                                      None                                  None                                      None                                   None                                       None                                   None                                       None                                   None                                       None                                  None                                      None                                   None                                       None                                  None                                      None                                   None                                       None                                   None                                       \n" 
7846          ] 
7847          # Check the created theta file. 
7848          lines = theta_file.readlines() 
7849          for i in range(len(lines)): 
7850              # Test lines starting with # 
7851              if theta_result[i][0] == "#": 
7852                  self.assertEqual(theta_result[i], lines[i]) 
7853              # If the line is equal each other, make a line comparison. This should catch lines with None values. 
7854              if theta_result[i] == lines[i]: 
7855                  self.assertEqual(theta_result[i], lines[i]) 
7856              # If the line is not equal each other, make a slower comparison of values. 
7857              else: 
7858                  # Print lines if they don't match. To help find differences. 
7859                  print(theta_result[i]) 
7860                  print(lines[i]) 
7861   
7862                  # First test first 62 characters containing spin information 
7863                  self.assertEqual(theta_result[i][:62], lines[i][:62]) 
7864   
7865                  # Make a string split after 62 characters. Select each second element, so None values are skipped. 
7866                  theta_result_s = theta_result[i][62:].split()[::2] 
7867                  print(theta_result_s ) 
7868                  lines_s = lines[i][62:].split()[::2] 
7869                  print(lines_s) 
7870                  # Loop over the value elements 
7871                  for j in range(len(lines_s)): 
7872                      print(theta_result_s[j], lines_s[j]) 
7873                      # Assume a precision to digits. 
7874                      self.assertAlmostEqual(float(theta_result_s[j]), float(lines_s[j]), 14) 
7875   
7876          # Close file 
7877          theta_file.close() 
7878   
7879          w_eff_file = open(w_eff_filepath, 'r') 
7880          w_eff_result = [ 
7881              "# Parameter description:  Effective field in rotating frame : ( w_eff = sqrt(Omega^2 + w_1^2) ) (rad.s^-1).\n", 
7882              "#\n", 
7883              "# mol_name    res_num    res_name    spin_num    spin_name    r1rho_799.77739910_118.078_1341.110    sd(r1rho_799.77739910_118.078_1341.110)    r1rho_799.77739910_118.078_1648.500    sd(r1rho_799.77739910_118.078_1648.500)    r1rho_799.77739910_118.078_431.000    sd(r1rho_799.77739910_118.078_431.000)    r1rho_799.77739910_118.078_651.200    sd(r1rho_799.77739910_118.078_651.200)    r1rho_799.77739910_118.078_800.500    sd(r1rho_799.77739910_118.078_800.500)    r1rho_799.77739910_118.078_984.000    sd(r1rho_799.77739910_118.078_984.000)    r1rho_799.77739910_124.247_1341.110    sd(r1rho_799.77739910_124.247_1341.110)    r1rho_799.77739910_130.416_1341.110    sd(r1rho_799.77739910_130.416_1341.110)    r1rho_799.77739910_130.416_1648.500    sd(r1rho_799.77739910_130.416_1648.500)    r1rho_799.77739910_130.416_800.500    sd(r1rho_799.77739910_130.416_800.500)    r1rho_799.77739910_142.754_1341.110    sd(r1rho_799.77739910_142.754_1341.110)    r1rho_799.77739910_142.754_800.500    sd(r1rho_799.77739910_142.754_800.500)    r1rho_799.77739910_179.768_1341.110    sd(r1rho_799.77739910_179.768_1341.110)    r1rho_799.77739910_241.459_1341.110    sd(r1rho_799.77739910_241.459_1341.110)    \n", 
7884              "None          5          I           None        N            None                                   None                                       None                                   None                                       None                                  None                                      None                                  None                                      None                                  None                                      None                                  None                                      None                                   None                                       None                                   None                                       None                                   None                                       None                                  None                                      None                                   None                                       None                                  None                                      None                                   None                                       None                                   None                                       \n", 
7885              "None          6          S           None        N            None                                   None                                       None                                   None                                       None                                  None                                      None                                  None                                      None                                  None                                      None                                  None                                      None                                   None                                       None                                   None                                       None                                   None                                       None                                  None                                      None                                   None                                       None                                  None                                      None                                   None                                       None                                   None                                       \n", 
7886              "None          8          S           None        N            None                                   None                                       None                                   None                                       None                                  None                                      None                                  None                                      None                                  None                                      None                                  None                                      None                                   None                                       None                                   None                                       None                                   None                                       None                                  None                                      None                                   None                                       None                                  None                                      None                                   None                                       None                                   None                                       \n", 
7887              "None          9          A           None        N            None                                   None                                       None                                   None                                       None                                  None                                      None                                  None                                      None                                  None                                      None                                  None                                      None                                   None                                       None                                   None                                       None                                   None                                       None                                  None                                      None                                   None                                       None                                  None                                      None                                   None                                       None                                   None                                       \n", 
7888              "None          10         L           None        N            None                                   None                                       None                                   None                                       None                                  None                                      None                                  None                                      None                                  None                                      None                                  None                                      None                                   None                                       None                                   None                                       None                                   None                                       None                                  None                                      None                                   None                                       None                                  None                                      None                                   None                                       None                                   None                                       \n", 
7889              "None          11         Q           None        N            None                                   None                                       None                                   None                                       None                                  None                                      None                                  None                                      None                                  None                                      None                                  None                                      None                                   None                                       None                                   None                                       None                                   None                                       None                                  None                                      None                                   None                                       None                                  None                                      None                                   None                                       None                                   None                                       \n", 
7890              "None          12         D           None        N            None                                   None                                       None                                   None                                       None                                  None                                      None                                  None                                      None                                  None                                      None                                  None                                      None                                   None                                       None                                   None                                       None                                   None                                       None                                  None                                      None                                   None                                       None                                  None                                      None                                   None                                       None                                   None                                       \n", 
7891              "None          13         L           None        N                8737.12883908829                   None                                           10612.1226552258                   None                                           3558.93734069587                  None                                          4698.27194621826                  None                                          5534.46153956037                  None                                          6599.82570817753                  None                                          8467.62674839481                   None                                           9318.00441649087                   None                                           11095.2662520767                   None                                           6412.33580591254                  None                                          13279.9803044242                   None                                            11430.254637056                  None                                          30318.7268264644                   None                                           61141.1080046448                   None                                       \n", 
7892              "None          14         L           None        N            None                                   None                                       None                                   None                                       None                                  None                                      None                                  None                                      None                                  None                                      None                                  None                                      None                                   None                                       None                                   None                                       None                                   None                                       None                                  None                                      None                                   None                                       None                                  None                                      None                                   None                                       None                                   None                                       \n", 
7893              "None          15         R           None        N                8427.14155005377                   None                                           10358.3995676635                   None                                           2710.22680763322                  None                                          4093.04942975722                  None                                          5030.86065069262                  None                                          6183.60685459024                  None                                          8956.28403254202                   None                                           10448.6627754369                   None                                           12060.4428066937                   None                                           7966.64282975241                  None                                          15045.8392092364                   None                                           13441.3586252373                  None                                          32438.4764809909                   None                                           63321.5201471181                   None                                       \n", 
7894              "None          16         T           None        N                 8536.7818857229                   None                                            10447.792678989                   None                                           3034.01707453628                  None                                           4314.2767521567                  None                                          5212.43600885913                  None                                          6332.21319855067                  None                                          9558.14311447582                   None                                           11384.2336494604                   None                                           12879.4604966293                   None                                           9159.34604475399                  None                                          16290.1746838959                   None                                           14821.0200530829                  None                                          33866.5933527757                   None                                           64785.3205696403                   None                                       \n", 
7895              "None          17         L           None        N            None                                   None                                       None                                   None                                       None                                  None                                      None                                  None                                      None                                  None                                      None                                  None                                      None                                   None                                       None                                   None                                       None                                   None                                       None                                  None                                      None                                   None                                       None                                  None                                      None                                   None                                       None                                   None                                       \n", 
7896              "None          18         K           None        N            None                                   None                                       None                                   None                                       None                                  None                                      None                                  None                                      None                                  None                                      None                                  None                                      None                                   None                                       None                                   None                                       None                                   None                                       None                                  None                                      None                                   None                                       None                                  None                                      None                                   None                                       None                                   None                                       \n", 
7897              "None          19         S           None        N            None                                   None                                       None                                   None                                       None                                  None                                      None                                  None                                      None                                  None                                      None                                  None                                      None                                   None                                       None                                   None                                       None                                   None                                       None                                  None                                      None                                   None                                       None                                  None                                      None                                   None                                       None                                   None                                       \n", 
7898              "None          21         S           None        N            None                                   None                                       None                                   None                                       None                                  None                                      None                                  None                                      None                                  None                                      None                                  None                                      None                                   None                                       None                                   None                                       None                                   None                                       None                                  None                                      None                                   None                                       None                                  None                                      None                                   None                                       None                                   None                                       \n", 
7899              "None          24         Q           None        N            None                                   None                                       None                                   None                                       None                                  None                                      None                                  None                                      None                                  None                                      None                                  None                                      None                                   None                                       None                                   None                                       None                                   None                                       None                                  None                                      None                                   None                                       None                                  None                                      None                                   None                                       None                                   None                                       \n", 
7900              "None          25         Q           None        N                8685.60895531182                   None                                           10569.7459677762                   None                                           3430.51272680396                  None                                          4601.75421490393                  None                                          5452.76508815826                  None                                          6531.46859076009                  None                                          8490.06475886501                   None                                           9406.58372902508                   None                                           11169.7602637607                   None                                           6540.38696356753                  None                                          13437.7348017798                   None                                           11613.1632549021                  None                                          30514.0741594726                   None                                           61342.4792156782                   None                                       \n", 
7901              "None          26         Q           None        N                8433.35533683544                   None                                           10363.4554631194                   None                                           2729.48656005151                  None                                          4105.82770792005                  None                                          5041.26238350827                  None                                          6192.07245313098                  None                                          8880.08366342131                   None                                           10312.6868786802                   None                                           11942.8320576165                   None                                           7787.44854491812                  None                                          14853.4987024375                   None                                           13225.7048162038                  None                                          32213.6690023282                   None                                           63090.7407990801                   None                                       \n", 
7902              "None          27         Q           None        N            None                                   None                                       None                                   None                                       None                                  None                                      None                                  None                                      None                                  None                                      None                                  None                                      None                                   None                                       None                                   None                                       None                                   None                                       None                                  None                                      None                                   None                                       None                                  None                                      None                                   None                                       None                                   None                                       \n", 
7903              "None          28         Q           None        N                8454.18308422202                   None                                           10380.4112885894                   None                                           2793.17494362899                  None                                          4148.43953208179                  None                                          5076.02756135055                  None                                          6220.40920270029                  None                                          8777.91538040813                   None                                           10118.8737706315                   None                                           11775.8792998529                   None                                           7528.90766101027                  None                                          14572.4015102398                   None                                            12909.211050939                  None                                          31882.8171856889                   None                                           62750.9120842199                   None                                       \n", 
7904              "None          29         V           None        N            None                                   None                                       None                                   None                                       None                                  None                                      None                                  None                                      None                                  None                                      None                                  None                                      None                                   None                                       None                                   None                                       None                                   None                                       None                                  None                                      None                                   None                                       None                                  None                                      None                                   None                                       None                                   None                                       \n", 
7905              "None          30         L           None        N            None                                   None                                       None                                   None                                       None                                  None                                      None                                  None                                      None                                  None                                      None                                  None                                      None                                   None                                       None                                   None                                       None                                   None                                       None                                  None                                      None                                   None                                       None                                  None                                      None                                   None                                       None                                   None                                       \n", 
7906              "None          31         N           None        N            None                                   None                                       None                                   None                                       None                                  None                                      None                                  None                                      None                                  None                                      None                                  None                                      None                                   None                                       None                                   None                                       None                                   None                                       None                                  None                                      None                                   None                                       None                                  None                                      None                                   None                                       None                                   None                                       \n", 
7907              "None          32         I           None        N            None                                   None                                       None                                   None                                       None                                  None                                      None                                  None                                      None                                  None                                      None                                  None                                      None                                   None                                       None                                   None                                       None                                   None                                       None                                  None                                      None                                   None                                       None                                  None                                      None                                   None                                       None                                   None                                       \n", 
7908              "None          33         L           None        N            None                                   None                                       None                                   None                                       None                                  None                                      None                                  None                                      None                                  None                                      None                                  None                                      None                                   None                                       None                                   None                                       None                                   None                                       None                                  None                                      None                                   None                                       None                                  None                                      None                                   None                                       None                                   None                                       \n", 
7909              "None          34         K           None        N            None                                   None                                       None                                   None                                       None                                  None                                      None                                  None                                      None                                  None                                      None                                  None                                      None                                   None                                       None                                   None                                       None                                   None                                       None                                  None                                      None                                   None                                       None                                  None                                      None                                   None                                       None                                   None                                       \n", 
7910              "None          35         S           None        N            None                                   None                                       None                                   None                                       None                                  None                                      None                                  None                                      None                                  None                                      None                                  None                                      None                                   None                                       None                                   None                                       None                                   None                                       None                                  None                                      None                                   None                                       None                                  None                                      None                                   None                                       None                                   None                                       \n", 
7911              "None          36         N           None        N            None                                   None                                       None                                   None                                       None                                  None                                      None                                  None                                      None                                  None                                      None                                  None                                      None                                   None                                       None                                   None                                       None                                   None                                       None                                  None                                      None                                   None                                       None                                  None                                      None                                   None                                       None                                   None                                       \n", 
7912              "None          38         Q           None        N            None                                   None                                       None                                   None                                       None                                  None                                      None                                  None                                      None                                  None                                      None                                  None                                      None                                   None                                       None                                   None                                       None                                   None                                       None                                  None                                      None                                   None                                       None                                  None                                      None                                   None                                       None                                   None                                       \n", 
7913              "None          39         L           None        N                 8586.6405431352                   None                                           10488.5710521378                   None                                           3171.59430904777                  None                                          4412.11227722123                  None                                          5293.69814015286                  None                                          6399.27143075725                  None                                          8557.58926327909                   None                                           9617.45773774313                   None                                           11347.9169998729                   None                                           6840.20010813426                  None                                          13795.1250622375                   None                                           12024.9041436853                  None                                           30951.651485352                   None                                           61793.2130509111                   None                                       \n", 
7914              "None          40         M           None        N                8427.90394711227                   None                                           10359.0198301036                   None                                           2712.59646573568                  None                                          4094.61889210019                  None                                          5032.13762965554                  None                                           6184.6458240746                  None                                          9049.68452800053                   None                                           10607.7913029633                   None                                           12198.5639821231                   None                                           8174.23271685285                  None                                          15266.4924700447                   None                                           13687.9010998756                  None                                          32694.9043143038                   None                                           63584.6371927381                   None                                       \n", 
7915              "None          41         A           None        N                8480.14299737436                   None                                           10401.5648897003                   None                                           2870.79081440785                  None                                          4201.09083283266                  None                                          5119.14733505123                  None                                          6255.64579267482                  None                                          8706.50768957471                   None                                           9972.71017314947                   None                                           11650.5225246067                   None                                           7331.28858930568                  None                                          14354.1616183112                   None                                           12662.3378547029                  None                                          31623.9195264738                   None                                           62484.8290612112                   None                                       \n", 
7916              "None          42         A           None        N            None                                   None                                       None                                   None                                       None                                  None                                      None                                  None                                      None                                  None                                      None                                  None                                      None                                   None                                       None                                   None                                       None                                   None                                       None                                  None                                      None                                   None                                       None                                  None                                      None                                   None                                       None                                   None                                       \n", 
7917              "None          43         F           None        N                8427.30062786474                   None                                           10358.5289868368                   None                                            2710.7214015056                  None                                          4093.37694357637                  None                                          5031.12711571215                  None                                          6183.82364721878                  None                                          8952.31975962078                   None                                           10441.7375680915                   None                                           12054.4435931163                   None                                           7957.55789315654                  None                                          15036.1316712316                   None                                           13430.4914212645                  None                                          32427.1596037519                   None                                           63309.9050677925                   None                                       \n", 
7918              "None          44         I           None        N                8426.54623319716                   None                                           10357.9152496503                   None                                            2708.3751705368                  None                                          4091.82359712664                  None                                          5029.86337809029                  None                                          6182.79552045043                  None                                          8979.12144335458                   None                                           10488.2688526334                   None                                           12094.7720286018                   None                                           8018.51779989075                  None                                          15101.1843990883                   None                                           13503.2816173444                  None                                          32502.9389163062                   None                                           63387.6763306952                   None                                       \n", 
7919              "None          45         K           None        N                8599.01176345321                   None                                           10498.7013581079                   None                                           3204.93649737055                  None                                          4436.14046641897                  None                                          5313.74138343704                  None                                          6415.86177652694                  None                                          8546.79665373249                   None                                           9587.16245449134                   None                                           11322.2529042385                   None                                           6797.53838612575                  None                                          13745.1536613763                   None                                           11967.5433300612                  None                                          30890.8603419261                   None                                           61730.6213936947                   None                                       \n", 
7920              "None          46         Q           None        N            None                                   None                                       None                                   None                                       None                                  None                                      None                                  None                                      None                                  None                                      None                                  None                                      None                                   None                                       None                                   None                                       None                                   None                                       None                                  None                                      None                                   None                                       None                                  None                                      None                                   None                                       None                                   None                                       \n", 
7921              "None          48         T           None        N            None                                   None                                       None                                   None                                       None                                  None                                      None                                  None                                      None                                  None                                      None                                  None                                      None                                   None                                       None                                   None                                       None                                   None                                       None                                  None                                      None                                   None                                       None                                  None                                      None                                   None                                       None                                   None                                       \n", 
7922              "None          49         A           None        N                9279.63849130869                   None                                           11063.0654625247                   None                                           4737.11992391463                  None                                          5643.40583860235                  None                                          6356.45614406507                  None                                          7302.87406141381                  None                                          8459.17105047661                   None                                           8761.54554569995                   None                                           10632.2343488142                   None                                           5572.92782399155                  None                                          12102.1714908775                   None                                           10037.6988885228                  None                                          28806.6916858172                   None                                           59579.0348769179                   None                                       \n", 
7923              "None          50         K           None        N            None                                   None                                       None                                   None                                       None                                  None                                      None                                  None                                      None                                  None                                      None                                  None                                      None                                   None                                       None                                   None                                       None                                   None                                       None                                  None                                      None                                   None                                       None                                  None                                      None                                   None                                       None                                   None                                       \n", 
7924              "None          51         Y           None        N            None                                   None                                       None                                   None                                       None                                  None                                      None                                  None                                      None                                  None                                      None                                  None                                      None                                   None                                       None                                   None                                       None                                   None                                       None                                  None                                      None                                   None                                       None                                  None                                      None                                   None                                       None                                   None                                       \n", 
7925              "None          52         V           None        N                8704.45610117774                   None                                           10585.2389163429                   None                                            3477.9549539207                  None                                          4637.22923167743                  None                                          5482.73656118686                  None                                           6556.5108895527                  None                                          8481.06470969555                   None                                           9372.86414918436                   None                                           11141.3782476763                   None                                           6491.79686536093                  None                                          13378.2843939736                   None                                           11544.3205736882                  None                                            30440.62308788                   None                                           61266.7742546508                   None                                       \n", 
7926              "None          53         A           None        N                9497.02860450276                   None                                           11246.0339326126                   None                                           5149.96766581255                  None                                          5994.15475647208                  None                                          6669.81232845336                  None                                          7577.19152075731                  None                                          8516.77431951689                   None                                           8639.36099840319                   None                                           10531.7750336522                   None                                           5378.79193153767                  None                                          11752.8060152439                   None                                           9613.59939949642                  None                                          28334.9153747994                   None                                           59090.2988815445                   None                                       \n", 
7927              "None          54         N           None        N            None                                   None                                       None                                   None                                       None                                  None                                      None                                  None                                      None                                  None                                      None                                  None                                      None                                   None                                       None                                   None                                       None                                   None                                       None                                  None                                      None                                   None                                       None                                  None                                      None                                   None                                       None                                   None                                       \n", 
7928              "None          55         Q           None        N            None                                   None                                       None                                   None                                       None                                  None                                      None                                  None                                      None                                  None                                      None                                  None                                      None                                   None                                       None                                   None                                       None                                   None                                       None                                  None                                      None                                   None                                       None                                  None                                      None                                   None                                       None                                   None                                       \n", 
7929              "None          57         G           None        N            None                                   None                                       None                                   None                                       None                                  None                                      None                                  None                                      None                                  None                                      None                                  None                                      None                                   None                                       None                                   None                                       None                                   None                                       None                                  None                                      None                                   None                                       None                                  None                                      None                                   None                                       None                                   None                                       \n", 
7930              "None          58         M           None        N            None                                   None                                       None                                   None                                       None                                  None                                      None                                  None                                      None                                  None                                      None                                  None                                      None                                   None                                       None                                   None                                       None                                   None                                       None                                  None                                      None                                   None                                       None                                  None                                      None                                   None                                       None                                   None                                       \n", 
7931              "None          59         Q           None        N            None                                   None                                       None                                   None                                       None                                  None                                      None                                  None                                      None                                  None                                      None                                  None                                      None                                   None                                       None                                   None                                       None                                   None                                       None                                  None                                      None                                   None                                       None                                  None                                      None                                   None                                       None                                   None                                       \n" 
7932          ] 
7933          # Check the created w_eff file. 
7934          lines = w_eff_file.readlines() 
7935          for i in range(len(lines)): 
7936              # Test lines starting with # 
7937              if w_eff_result[i][0] == "#": 
7938                  self.assertEqual(w_eff_result[i], lines[i]) 
7939              # If the line is equal each other, make a line comparison. This should catch lines with None values. 
7940              if w_eff_result[i] == lines[i]: 
7941                  self.assertEqual(w_eff_result[i], lines[i]) 
7942              # If the line is not equal each other, make a slower comparison of values. 
7943              else: 
7944                  # Print lines if they don't match. To help find differences. 
7945                  print(w_eff_result[i]) 
7946                  print(lines[i]) 
7947   
7948                  # First test first 62 characters containing spin information 
7949                  self.assertEqual(w_eff_result[i][:62], lines[i][:62]) 
7950   
7951                  # Make a string split after 62 characters. Select each second element, so None values are skipped. 
7952                  w_eff_result_s = w_eff_result[i][62:].split()[::2] 
7953                  print(w_eff_result_s ) 
7954                  lines_s = lines[i][62:].split()[::2] 
7955                  print(lines_s) 
7956                  # Loop over the value elements 
7957                  for j in range(len(lines_s)): 
7958                      print(w_eff_result_s[j], lines_s[j]) 
7959                      # Assume a precision to digits. 
7960                      self.assertAlmostEqual(float(w_eff_result_s[j]), float(lines_s[j]), 14) 
7961   
7962          # Close file 
7963          w_eff_file.close() 
7964   
7965   
7966 -    def verify_estimate_r2eff_err_compare_mc(self): 
7967          """Test the user function for estimating R2eff errors from exponential curve fitting, and compare it with Monte-Carlo simulations. 
7968   
7969          This follows Task 7822. 
7970          U{task #7822<https://gna.org/task/index.php?7822>}: Implement user function to estimate R2eff and associated errors for exponential curve fitting. 
7971   
7972          This uses the data from Kjaergaard's paper at U{DOI: 10.1021/bi4001062<http://dx.doi.org/10.1021/bi4001062>}. 
7973          Optimisation of the Kjaergaard et al., 2013 Off-resonance R1rho relaxation dispersion experiments using the 'DPL' model. 
7974          """ 
7975   
7976          # Load the data. 
7977          data_path = status.install_path + sep+'test_suite'+sep+'shared_data'+sep+'dispersion'+sep+'Kjaergaard_et_al_2013'+sep 
7978   
7979          # Set pipe name, bundle and type. 
7980          pipe_name = 'base pipe' 
7981          pipe_bundle = 'relax_disp' 
7982          pipe_type = 'relax_disp' 
7983   
7984          # Create the data pipe. 
7985          self.interpreter.pipe.create(pipe_name=pipe_name, bundle=pipe_bundle, pipe_type=pipe_type) 
7986   
7987          file = data_path + '1_setup_r1rho_GUI.py' 
7988          self.interpreter.script(file=file, dir=None) 
7989   
7990          # Deselect all spins. 
7991          self.interpreter.deselect.spin(spin_id=':1-100', change_all=False) 
7992   
7993          # Select one spin. 
7994          self.interpreter.select.spin(spin_id=':52@N', change_all=False) 
7995   
7996          # Set the model. 
7997          self.interpreter.relax_disp.select_model(MODEL_R2EFF) 
7998   
7999          # Check if intensity errors have already been calculated. 
8000          check_intensity_errors() 
8001   
8002          # Do a grid search. 
8003          self.interpreter.minimise.grid_search(lower=None, upper=None, inc=11, constraints=True, verbosity=1) 
8004   
8005          # Set algorithm. 
8006          min_algor = 'Newton' 
8007          constraints = True 
8008          if constraints: 
8009              min_options = ('%s'%(min_algor),) 
8010              #min_algor = 'Log barrier' 
8011              min_algor = 'Method of Multipliers' 
8012              scaling_matrix = assemble_scaling_matrix(scaling=True) 
8013   
8014              # Collect spins 
8015              all_spin_ids = [] 
8016              for cur_spin, mol_name, resi, resn, spin_id in spin_loop(full_info=True, return_id=True, skip_desel=True): 
8017                  all_spin_ids.append(spin_id) 
8018   
8019              spins = spin_ids_to_containers(all_spin_ids[:1]) 
8020   
8021              # Get constraints 
8022              A, b = linear_constraints(spins=spins, scaling_matrix=scaling_matrix[0]) 
8023          else: 
8024              min_options = () 
8025              A, b = None, None 
8026          min_options = () 
8027          sim_boot = 200 
8028          scaling_list = [1.0, 1.0] 
8029   
8030          # Minimise. 
8031          self.interpreter.minimise.execute(min_algor=min_algor, constraints=constraints, verbosity=1) 
8032   
8033          # Loop over old err attributes. 
8034          err_attr_list = ['r2eff_err', 'i0_err'] 
8035   
8036          for cur_spin, mol_name, resi, resn, spin_id in spin_loop(full_info=True, return_id=True, skip_desel=True): 
8037              # Loop over old err attributes. 
8038              for err_attr in err_attr_list: 
8039                  if hasattr(cur_spin, err_attr): 
8040                      delattr(cur_spin, err_attr) 
8041   
8042          # Collect the estimation data from boot. 
8043          my_dic = {} 
8044          param_key_list = [] 
8045          est_keys = [] 
8046          est_key = '-2' 
8047          est_keys.append(est_key) 
8048          spin_id_list = [] 
8049   
8050          for cur_spin, mol_name, resi, resn, spin_id in spin_loop(full_info=True, return_id=True, skip_desel=True): 
8051              # Add key to dic. 
8052              my_dic[spin_id] = {} 
8053   
8054              # Add key for estimate. 
8055              my_dic[spin_id][est_key] = {} 
8056   
8057              # Add spin key to list. 
8058              spin_id_list.append(spin_id) 
8059   
8060              # Generate spin string. 
8061              spin_string = generate_spin_string(spin=cur_spin, mol_name=mol_name, res_num=resi, res_name=resn) 
8062   
8063              for exp_type, frq, offset, point, ei, mi, oi, di in loop_exp_frq_offset_point(return_indices=True): 
8064                  # Generate the param_key. 
8065                  param_key = return_param_key_from_data(exp_type=exp_type, frq=frq, offset=offset, point=point) 
8066   
8067                  # Append key. 
8068                  param_key_list.append(param_key) 
8069   
8070                  # Add key to dic. 
8071                  my_dic[spin_id][est_key][param_key] = {} 
8072   
8073                  values = [] 
8074                  errors = [] 
8075                  times = [] 
8076                  for time in loop_time(exp_type=exp_type, frq=frq, offset=offset, point=point): 
8077                      values.append(average_intensity(spin=cur_spin, exp_type=exp_type, frq=frq, offset=offset, point=point, time=time)) 
8078                      errors.append(average_intensity(spin=cur_spin, exp_type=exp_type, frq=frq, offset=offset, point=point, time=time, error=True)) 
8079                      times.append(time) 
8080   
8081                  # Convert to numpy array. 
8082                  values = asarray(values) 
8083                  errors = asarray(errors) 
8084                  times = asarray(times) 
8085   
8086                  r2eff = getattr(cur_spin, 'r2eff')[param_key] 
8087                  i0 = getattr(cur_spin, 'i0')[param_key] 
8088   
8089                  R_m_sim_l = [] 
8090                  I0_m_sim_l = [] 
8091                  for j in range(sim_boot): 
8092                      if j in range(0, 100000, 100): 
8093                          print("Simulation %i"%j) 
8094                      # Start minimisation. 
8095   
8096                      # Produce errors 
8097                      I_err = [] 
8098                      for j, error in enumerate(errors): 
8099                          I_error = gauss(values[j], error) 
8100                          I_err.append(I_error) 
8101                      # Convert to numpy array. 
8102                      I_err = asarray(I_err) 
8103   
8104                      x0 = [r2eff, i0] 
8105                      setup(num_params=len(x0), num_times=len(times), values=I_err, sd=errors, relax_times=times, scaling_matrix=scaling_list) 
8106   
8107                      # Ref input. 
8108                      #def generic_minimise(func=None, dfunc=None, d2func=None, args=(), x0=None, min_algor=None, min_options=None, func_tol=1e-25, grad_tol=None, maxiter=1e6, A=None, b=None, l=None, u=None, c=None, dc=None, d2c=None, print_flag=0, print_prefix="", full_output=False): 
8109                      # l=l, u=u, c=c, dc=dc, d2c=d2c 
8110                      # l: Lower bound constraint vector (l <= x <= u). 
8111                      # u: Upper bound constraint vector (l <= x <= u). 
8112                      # c: User supplied constraint function. 
8113                      # dc: User supplied constraint gradient function. 
8114                      params_minfx_sim_j, chi2_minfx_sim_j, iter_count, f_count, g_count, h_count, warning = generic_minimise(func=func, dfunc=dfunc, d2func=d2func, args=(), x0=x0, min_algor=min_algor, min_options=min_options, A=A, b=b, full_output=True, print_flag=0) 
8115   
8116                      R_m_sim_j, I0_m_sim_j = params_minfx_sim_j 
8117                      R_m_sim_l.append(R_m_sim_j) 
8118                      I0_m_sim_l.append(I0_m_sim_j) 
8119   
8120                  # Get stats on distribution. 
8121                  sigma_R_sim = std(asarray(R_m_sim_l), ddof=1) 
8122                  sigma_I0_sim = std(asarray(I0_m_sim_l), ddof=1) 
8123                  my_dic[spin_id][est_key][param_key]['r2eff_err'] = sigma_R_sim 
8124                  my_dic[spin_id][est_key][param_key]['i0_err'] = sigma_I0_sim 
8125   
8126          # Estimate R2eff errors. 
8127          self.interpreter.relax_disp.r2eff_err_estimate() 
8128   
8129          est_key = '-1' 
8130          est_keys.append(est_key) 
8131   
8132          # Collect data. 
8133          for cur_spin, mol_name, resi, resn, spin_id in spin_loop(full_info=True, return_id=True, skip_desel=True): 
8134              # Add key for estimate. 
8135              my_dic[spin_id][est_key] = {} 
8136   
8137              for exp_type, frq, offset, point, ei, mi, oi, di in loop_exp_frq_offset_point(return_indices=True): 
8138                  # Generate the param_key. 
8139                  param_key = return_param_key_from_data(exp_type=exp_type, frq=frq, offset=offset, point=point) 
8140   
8141                  # Add key to dic. 
8142                  my_dic[spin_id][est_key][param_key] = {} 
8143   
8144                  # Get the value. 
8145                  # Loop over err attributes. 
8146                  for err_attr in err_attr_list: 
8147                      if hasattr(cur_spin, err_attr): 
8148                          get_err_attr = getattr(cur_spin, err_attr)[param_key] 
8149                      else: 
8150                          get_err_attr = 0.0 
8151   
8152                      # Save to dic. 
8153                      my_dic[spin_id][est_key][param_key][err_attr] = get_err_attr 
8154   
8155   
8156          # Make Carlo Simulations number 
8157          mc_number_list = list(range(0, 1000, 250)) 
8158   
8159          sim_attr_list = ['chi2_sim', 'f_count_sim', 'g_count_sim', 'h_count_sim', 'i0_sim', 'iter_sim', 'peak_intensity_sim', 'r2eff_sim', 'select_sim', 'warning_sim'] 
8160   
8161          # Loop over the Monte Carlo simulations: 
8162          for number in mc_number_list: 
8163              # First delete old simulations. 
8164              for cur_spin, mol_name, resi, resn, spin_id in spin_loop(full_info=True, return_id=True, skip_desel=True): 
8165                  # Loop over old err attributes. 
8166                  for err_attr in err_attr_list: 
8167                      if hasattr(cur_spin, err_attr): 
8168                          delattr(cur_spin, err_attr) 
8169   
8170                  # Loop over the simulated attributes. 
8171                  for sim_attr in sim_attr_list: 
8172                      if hasattr(cur_spin, sim_attr): 
8173                          delattr(cur_spin, sim_attr) 
8174   
8175              self.interpreter.monte_carlo.setup(number=number) 
8176              self.interpreter.monte_carlo.create_data() 
8177              self.interpreter.monte_carlo.initial_values() 
8178              self.interpreter.minimise.execute(min_algor=min_algor, constraints=constraints) 
8179              self.interpreter.eliminate() 
8180              self.interpreter.monte_carlo.error_analysis() 
8181   
8182              est_key = '%i'%number 
8183              est_keys.append(est_key) 
8184   
8185              # Collect data. 
8186              for cur_spin, mol_name, resi, resn, spin_id in spin_loop(full_info=True, return_id=True, skip_desel=True): 
8187                  # Add key for estimate. 
8188                  my_dic[spin_id][est_key] = {} 
8189   
8190                  for exp_type, frq, offset, point, ei, mi, oi, di in loop_exp_frq_offset_point(return_indices=True): 
8191                      # Generate the param_key. 
8192                      param_key = return_param_key_from_data(exp_type=exp_type, frq=frq, offset=offset, point=point) 
8193   
8194                      # Add key to dic. 
8195                      my_dic[spin_id][est_key][param_key] = {} 
8196   
8197                      # Get the value. 
8198                      # Loop over err attributes. 
8199                      for err_attr in err_attr_list: 
8200                          if hasattr(cur_spin, err_attr): 
8201                              get_err_attr = getattr(cur_spin, err_attr)[param_key] 
8202                          else: 
8203                              get_err_attr = 0.0 
8204   
8205                          # Save to dic. 
8206                          my_dic[spin_id][est_key][param_key][err_attr] = get_err_attr 
8207   
8208          # Set what to extract. 
8209          err_attr = err_attr_list[0] 
8210   
8211          # Define list with text. 
8212          text_list = [] 
8213   
8214          # Now loop through the data. 
8215          for spin_id in spin_id_list: 
8216              for est_key in est_keys: 
8217                  # Define list to pickup data. 
8218                  r2eff_err_list = [] 
8219   
8220                  for param_key in param_key_list: 
8221                      # Get the value. 
8222                      r2eff_err = my_dic[spin_id][est_key][param_key][err_attr] 
8223   
8224                      # Add to list. 
8225                      r2eff_err_list.append(r2eff_err) 
8226   
8227                  # Sum the list 
8228                  sum_array = sum(array(r2eff_err_list)) 
8229   
8230                  # Join floats to string. 
8231                  r2eff_err_str = " ".join(format(x, "2.3f") for x in r2eff_err_list) 
8232   
8233                  # Define print string. 
8234                  text = "%8s %s sum= %2.3f" % (est_key, r2eff_err_str, sum_array) 
8235                  text_list.append(text) 
8236   
8237   
8238          # Now print. 
8239          filepath = NamedTemporaryFile(delete=False).name 
8240          # Open the files for testing. 
8241          w_file = open(filepath, 'w') 
8242   
8243          print("Printing the estimated R2eff error as function of estimation from Co-variance and number of Monte-Carlo simulations.") 
8244   
8245          for text in text_list: 
8246              # Print. 
8247              print(text) 
8248   
8249              # Write to file. 
8250              w_file.write(text+"\n") 
8251   
8252          # Close files 
8253          w_file.close() 
8254   
8255          print("Filepath is: %s"%filepath) 
8256          print("Start 'gnuplot' and write:") 
8257          print("set term dumb") 
8258          print("plot '%s' using 1:17 title 'R2eff error as function of MC number' w linespoints "%filepath) 
8259   
8260   
8261 -    def verify_r1rho_kjaergaard_missing_r1(self, models=None, result_dir_name=None, r2eff_estimate=None): 
8262          """Verification of test_r1rho_kjaergaard_missing_r1.""" 
8263   
8264          # Check the kex value of residue 52 
8265          #self.assertAlmostEqual(cdp.mol[0].res[41].spin[0].kex, ds.ref[':52@N'][6]) 
8266   
8267          # Print results for each model. 
8268          print("\n\n################") 
8269          print("Printing results") 
8270          print("################\n") 
8271          for model in models: 
8272              # Skip R2eff model. 
8273              if model == MODEL_R2EFF: 
8274                  continue 
8275   
8276              # Switch to pipe. 
8277              self.interpreter.pipe.switch(pipe_name='%s - relax_disp' % (model)) 
8278              print("\nModel: %s" % (model)) 
8279   
8280              # Loop over the spins. 
8281              for cur_spin, mol_name, resi, resn, spin_id in spin_loop(full_info=True, return_id=True, skip_desel=True): 
8282                  # Generate spin string. 
8283                  spin_string = generate_spin_string(spin=cur_spin, mol_name=mol_name, res_num=resi, res_name=resn) 
8284   
8285                  # Loop over the parameters. 
8286                  print("Optimised parameters for spin: %s" % (spin_string)) 
8287                  for param in cur_spin.params + ['chi2']: 
8288                      # Get the value. 
8289                      if param in ['r1', 'r2']: 
8290                          for exp_type, frq, ei, mi in loop_exp_frq(return_indices=True): 
8291                              # Generate the R20 key. 
8292                              r20_key = generate_r20_key(exp_type=exp_type, frq=frq) 
8293   
8294                              # Get the value. 
8295                              value = getattr(cur_spin, param)[r20_key] 
8296   
8297                              # Print value. 
8298                              print("%-10s %-6s %-6s %3.8f" % ("Parameter:", param, "Value:", value)) 
8299   
8300                              # Compare values. 
8301                              if spin_id == ':52@N': 
8302                                  if param == 'r1': 
8303                                      if model == MODEL_NOREX: 
8304                                          if r2eff_estimate == 'direct': 
8305                                              self.assertAlmostEqual(value, 1.46138805) 
8306                                          elif r2eff_estimate == 'MC2000': 
8307                                              self.assertAlmostEqual(value, 1.46328102) 
8308                                          elif r2eff_estimate == 'chi2_pyt': 
8309                                              self.assertAlmostEqual(value, 1.43820629) 
8310                                      elif model == MODEL_DPL94: 
8311                                          if r2eff_estimate == 'direct': 
8312                                              self.assertAlmostEqual(value, 1.44845742) 
8313                                          elif r2eff_estimate == 'MC2000': 
8314                                              self.assertAlmostEqual(value, 1.45019848) 
8315                                          elif r2eff_estimate == 'chi2_pyt': 
8316                                              self.assertAlmostEqual(value, 1.44666512) 
8317                                      elif model == MODEL_TP02: 
8318                                          if r2eff_estimate == 'direct': 
8319                                              self.assertAlmostEqual(value, 1.54354392) 
8320                                          elif r2eff_estimate == 'MC2000': 
8321                                              self.assertAlmostEqual(value, 1.54352369) 
8322                                          elif r2eff_estimate == 'chi2_pyt': 
8323                                              self.assertAlmostEqual(value, 1.55964020) 
8324                                      elif model == MODEL_TAP03: 
8325                                          if r2eff_estimate == 'direct': 
8326                                              self.assertAlmostEqual(value, 1.54356410) 
8327                                          elif r2eff_estimate == 'MC2000': 
8328                                              self.assertAlmostEqual(value, 1.54354367) 
8329                                          elif r2eff_estimate == 'chi2_pyt': 
8330                                              self.assertAlmostEqual(value, 1.55967157) 
8331                                      elif model == MODEL_MP05: 
8332                                          if r2eff_estimate == 'direct': 
8333                                              self.assertAlmostEqual(value, 1.54356416) 
8334                                          elif r2eff_estimate == 'MC2000': 
8335                                              self.assertAlmostEqual(value, 1.54354372) 
8336                                          elif r2eff_estimate == 'chi2_pyt': 
8337                                              self.assertAlmostEqual(value, 1.55967163) 
8338                                      elif model == MODEL_NS_R1RHO_2SITE: 
8339                                          if r2eff_estimate == 'direct': 
8340                                              self.assertAlmostEqual(value, 1.41359221, 5) 
8341                                          elif r2eff_estimate == 'MC2000': 
8342                                              self.assertAlmostEqual(value, 1.41321968, 5) 
8343                                          elif r2eff_estimate == 'chi2_pyt': 
8344                                              self.assertAlmostEqual(value, 1.36303129, 5) 
8345   
8346                                  elif param == 'r2': 
8347                                      if model == MODEL_NOREX: 
8348                                          if r2eff_estimate == 'direct': 
8349                                              self.assertAlmostEqual(value, 11.48392439) 
8350                                          elif r2eff_estimate == 'MC2000': 
8351                                              self.assertAlmostEqual(value, 11.48040934) 
8352                                          elif r2eff_estimate == 'chi2_pyt': 
8353                                              self.assertAlmostEqual(value, 11.47224488) 
8354                                      elif model == MODEL_DPL94: 
8355                                          if r2eff_estimate == 'direct': 
8356                                              self.assertAlmostEqual(value, 10.15688372, 6) 
8357                                          elif r2eff_estimate == 'MC2000': 
8358                                              self.assertAlmostEqual(value, 10.16304887, 6) 
8359                                          elif r2eff_estimate == 'chi2_pyt': 
8360                                              self.assertAlmostEqual(value, 9.20037797, 6) 
8361                                      elif model == MODEL_TP02: 
8362                                          if r2eff_estimate == 'direct': 
8363                                              self.assertAlmostEqual(value, 9.72654896, 6) 
8364                                          elif r2eff_estimate == 'MC2000': 
8365                                              self.assertAlmostEqual(value, 9.72772726, 6) 
8366                                          elif r2eff_estimate == 'chi2_pyt': 
8367                                              self.assertAlmostEqual(value, 9.53948340, 6) 
8368                                      elif model == MODEL_TAP03: 
8369                                          if r2eff_estimate == 'direct': 
8370                                              self.assertAlmostEqual(value, 9.72641887, 6) 
8371                                          elif r2eff_estimate == 'MC2000': 
8372                                              self.assertAlmostEqual(value, 9.72759374, 6) 
8373                                          elif r2eff_estimate == 'chi2_pyt': 
8374                                              self.assertAlmostEqual(value, 9.53926913, 6) 
8375                                      elif model == MODEL_MP05: 
8376                                          if r2eff_estimate == 'direct': 
8377                                              self.assertAlmostEqual(value, 9.72641723, 6) 
8378                                          elif r2eff_estimate == 'MC2000': 
8379                                              self.assertAlmostEqual(value, 9.72759220, 6) 
8380                                          elif r2eff_estimate == 'chi2_pyt': 
8381                                              self.assertAlmostEqual(value, 9.53926778, 6) 
8382                                      elif model == MODEL_NS_R1RHO_2SITE: 
8383                                          if r2eff_estimate == 'direct': 
8384                                              self.assertAlmostEqual(value, 9.34531535, 5) 
8385                                          elif r2eff_estimate == 'MC2000': 
8386                                              self.assertAlmostEqual(value, 9.34602793, 5) 
8387                                          elif r2eff_estimate == 'chi2_pyt': 
8388                                              self.assertAlmostEqual(value, 9.17631409, 5) 
8389   
8390                      # For all other parameters. 
8391                      else: 
8392                          # Get the value. 
8393                          value = getattr(cur_spin, param) 
8394   
8395                          # Print value. 
8396                          print("%-10s %-6s %-6s %3.8f" % ("Parameter:", param, "Value:", value)) 
8397   
8398                          # Compare values. 
8399                          if spin_id == ':52@N': 
8400                              if param == 'phi_ex': 
8401                                  if model == MODEL_DPL94: 
8402                                      if r2eff_estimate == 'direct': 
8403                                          self.assertAlmostEqual(value, 0.07599563) 
8404                                      elif r2eff_estimate == 'MC2000': 
8405                                          self.assertAlmostEqual(value, 0.07561937) 
8406                                      elif r2eff_estimate == 'chi2_pyt': 
8407                                          self.assertAlmostEqual(value, 0.12946061) 
8408   
8409                              elif param == 'pA': 
8410                                  if model == MODEL_TP02: 
8411                                      if r2eff_estimate == 'direct': 
8412                                          self.assertAlmostEqual(value, 0.88827040) 
8413                                      elif r2eff_estimate == 'MC2000': 
8414                                          self.assertAlmostEqual(value, 0.88807487) 
8415                                      elif r2eff_estimate == 'chi2_pyt': 
8416                                          self.assertAlmostEqual(value, 0.87746233) 
8417                                  elif model == MODEL_TAP03: 
8418                                      if r2eff_estimate == 'direct': 
8419                                          self.assertAlmostEqual(value, 0.88828922) 
8420                                      elif r2eff_estimate == 'MC2000': 
8421                                          self.assertAlmostEqual(value, 0.88809318) 
8422                                      elif r2eff_estimate == 'chi2_pyt': 
8423                                          self.assertAlmostEqual(value, 0.87747558) 
8424                                  elif model == MODEL_MP05: 
8425                                      if r2eff_estimate == 'direct': 
8426                                          self.assertAlmostEqual(value, 0.88828924, 6) 
8427                                      elif r2eff_estimate == 'MC2000': 
8428                                          self.assertAlmostEqual(value, 0.88809321) 
8429                                      elif r2eff_estimate == 'chi2_pyt': 
8430                                          self.assertAlmostEqual(value, 0.87747562) 
8431                                  elif model == MODEL_NS_R1RHO_2SITE: 
8432                                      if r2eff_estimate == 'direct': 
8433                                          self.assertAlmostEqual(value, 0.94504369, 6) 
8434                                      elif r2eff_estimate == 'MC2000': 
8435                                          self.assertAlmostEqual(value, 0.94496541, 6) 
8436                                      elif r2eff_estimate == 'chi2_pyt': 
8437                                          self.assertAlmostEqual(value, 0.92084707, 6) 
8438   
8439                              elif param == 'dw': 
8440                                  if model == MODEL_TP02: 
8441                                      if r2eff_estimate == 'direct': 
8442                                          self.assertAlmostEqual(value, 1.08875840, 6) 
8443                                      elif r2eff_estimate == 'MC2000': 
8444                                          self.assertAlmostEqual(value, 1.08765638, 6) 
8445                                      elif r2eff_estimate == 'chi2_pyt': 
8446                                          self.assertAlmostEqual(value, 1.09753230, 6) 
8447                                  elif model == MODEL_TAP03: 
8448                                      if r2eff_estimate == 'direct': 
8449                                          self.assertAlmostEqual(value, 1.08837238, 6) 
8450                                      elif r2eff_estimate == 'MC2000': 
8451                                          self.assertAlmostEqual(value, 1.08726698, 6) 
8452                                      elif r2eff_estimate == 'chi2_pyt': 
8453                                          self.assertAlmostEqual(value, 1.09708821, 6) 
8454                                  elif model == MODEL_MP05: 
8455                                      if r2eff_estimate == 'direct': 
8456                                          self.assertAlmostEqual(value, 1.08837241, 6) 
8457                                      elif r2eff_estimate == 'MC2000': 
8458                                          self.assertAlmostEqual(value, 1.08726706, 6) 
8459                                      elif r2eff_estimate == 'chi2_pyt': 
8460                                          self.assertAlmostEqual(value, 1.09708832, 6) 
8461                                  elif model == MODEL_NS_R1RHO_2SITE: 
8462                                      if r2eff_estimate == 'direct': 
8463                                          self.assertAlmostEqual(value, 1.56001812, 5) 
8464                                      elif r2eff_estimate == 'MC2000': 
8465                                          self.assertAlmostEqual(value, 1.55833321, 5) 
8466                                      elif r2eff_estimate == 'chi2_pyt': 
8467                                          self.assertAlmostEqual(value, 1.36406712, 5) 
8468   
8469                              elif param == 'kex': 
8470                                  if model == MODEL_DPL94: 
8471                                      if r2eff_estimate == 'direct': 
8472                                          self.assertAlmostEqual(value/1e5, 4460.43711569/1e5, 7) 
8473                                      elif r2eff_estimate == 'MC2000': 
8474                                          self.assertAlmostEqual(value/1e5, 4419.03917195/1e5, 7) 
8475                                      elif r2eff_estimate == 'chi2_pyt': 
8476                                          self.assertAlmostEqual(value/1e5, 6790.22736344/1e5, 7) 
8477                                  elif model == MODEL_TP02: 
8478                                      if r2eff_estimate == 'direct': 
8479                                          self.assertAlmostEqual(value/1e5, 4921.28602757/1e5, 7) 
8480                                      elif r2eff_estimate == 'MC2000': 
8481                                          self.assertAlmostEqual(value/1e5, 4904.70144883/1e5, 7) 
8482                                      elif r2eff_estimate == 'chi2_pyt': 
8483                                          self.assertAlmostEqual(value/1e5, 5146.20306591/1e5, 7) 
8484                                  elif model == MODEL_TAP03: 
8485                                      if r2eff_estimate == 'direct': 
8486                                          self.assertAlmostEqual(value/1e5, 4926.42963491/1e5, 7) 
8487                                      elif r2eff_estimate == 'MC2000': 
8488                                          self.assertAlmostEqual(value/1e5, 4909.86877150/1e5, 7) 
8489                                      elif r2eff_estimate == 'chi2_pyt': 
8490                                          self.assertAlmostEqual(value/1e5, 5152.51105814/1e5, 7) 
8491                                  elif model == MODEL_MP05: 
8492                                      if r2eff_estimate == 'direct': 
8493                                          self.assertAlmostEqual(value/1e5, 4926.44236315/1e5, 7) 
8494                                      elif r2eff_estimate == 'MC2000': 
8495                                          self.assertAlmostEqual(value/1e5, 4909.88110195/1e5, 7) 
8496                                      elif r2eff_estimate == 'chi2_pyt': 
8497                                          self.assertAlmostEqual(value/1e5, 5152.52097111/1e5, 7) 
8498                                  elif model == MODEL_NS_R1RHO_2SITE: 
8499                                      if r2eff_estimate == 'direct': 
8500                                          self.assertAlmostEqual(value/1e5, 5628.66061488/1e5, 7) 
8501                                      elif r2eff_estimate == 'MC2000': 
8502                                          self.assertAlmostEqual(value/1e5, 5610.20221435/1e5, 6) 
8503                                      elif r2eff_estimate == 'chi2_pyt': 
8504                                          self.assertAlmostEqual(value/1e5, 5643.34067090/1e5, 6) 
8505   
8506                              elif param == 'chi2': 
8507                                  if model == MODEL_NOREX: 
8508                                      if r2eff_estimate == 'direct': 
8509                                          self.assertAlmostEqual(value, 848.42016907, 5) 
8510                                      elif r2eff_estimate == 'MC2000': 
8511                                          self.assertAlmostEqual(value, 3363.95829122, 5) 
8512                                      elif r2eff_estimate == 'chi2_pyt': 
8513                                          self.assertAlmostEqual(value, 5976.49946726, 5) 
8514                                  elif model == MODEL_DPL94: 
8515                                      if r2eff_estimate == 'direct': 
8516                                          self.assertAlmostEqual(value, 179.47041241) 
8517                                      elif r2eff_estimate == 'MC2000': 
8518                                          self.assertAlmostEqual(value, 710.24767560) 
8519                                      elif r2eff_estimate == 'chi2_pyt': 
8520                                          self.assertAlmostEqual(value, 612.72616697, 5) 
8521                                  elif model == MODEL_TP02: 
8522                                      if r2eff_estimate == 'direct': 
8523                                          self.assertAlmostEqual(value, 29.33882530, 6) 
8524                                      elif r2eff_estimate == 'MC2000': 
8525                                          self.assertAlmostEqual(value, 114.47142772, 6) 
8526                                      elif r2eff_estimate == 'chi2_pyt': 
8527                                          self.assertAlmostEqual(value, 250.50838162, 5) 
8528                                  elif model == MODEL_TAP03: 
8529                                      if r2eff_estimate == 'direct': 
8530                                          self.assertAlmostEqual(value, 29.29050673, 6) 
8531                                      elif r2eff_estimate == 'MC2000': 
8532                                          self.assertAlmostEqual(value, 114.27987534) 
8533                                      elif r2eff_estimate == 'chi2_pyt': 
8534                                          self.assertAlmostEqual(value, 250.04050719, 5) 
8535                                  elif model == MODEL_MP05: 
8536                                      if r2eff_estimate == 'direct': 
8537                                          self.assertAlmostEqual(value, 29.29054301, 6) 
8538                                      elif r2eff_estimate == 'MC2000': 
8539                                          self.assertAlmostEqual(value, 114.28002272) 
8540                                      elif r2eff_estimate == 'chi2_pyt': 
8541                                          self.assertAlmostEqual(value, 250.04077478, 5) 
8542                                  elif model == MODEL_NS_R1RHO_2SITE: 
8543                                      if r2eff_estimate == 'direct': 
8544                                          self.assertAlmostEqual(value, 34.44010543, 6) 
8545                                      elif r2eff_estimate == 'MC2000': 
8546                                          self.assertAlmostEqual(value, 134.14368365) 
8547                                      elif r2eff_estimate == 'chi2_pyt': 
8548                                          self.assertAlmostEqual(value, 278.55121388, 5) 
8549   
8550   
8551          # Print the final pipe. 
8552          model = 'final' 
8553          self.interpreter.pipe.switch(pipe_name='%s - relax_disp' % (model)) 
8554          print("\nFinal pipe") 
8555   
8556          # Loop over the spins. 
8557          for cur_spin, mol_name, resi, resn, spin_id in spin_loop(full_info=True, return_id=True, skip_desel=True): 
8558              # Generate spin string. 
8559              spin_string = generate_spin_string(spin=cur_spin, mol_name=mol_name, res_num=resi, res_name=resn) 
8560   
8561              # Loop over the parameters. 
8562              print("Optimised model for spin: %s" % (spin_string)) 
8563              param = 'model' 
8564   
8565              # Get the value. 
8566              value = getattr(cur_spin, param) 
8567              print("%-10s %-6s %-6s %6s" % ("Parameter:", param, "Value:", value)) 
8568   
8569   
8570          ### Now check some of the written out files. 
8571          file_names = ['r1rho_prime', 'r1'] 
8572   
8573          for file_name_i in file_names: 
8574   
8575              # Make the file name. 
8576              file_name = "%s.out" % file_name_i 
8577   
8578              # Get the file path. 
8579              file_path = get_file_path(file_name, result_dir_name + sep + model) 
8580   
8581              # Test the file exists. 
8582              print("Testing file access to: %s"%file_path) 
8583              self.assert_(access(file_path, F_OK)) 
8584   
8585              # Now open, and compare content, line by line. 
8586              file_prod = open(file_path) 
8587              lines_prod = file_prod.readlines() 
8588              file_prod.close() 
8589   
8590              # Loop over the lines. 
8591              for i, line in enumerate(lines_prod): 
8592                  # Make the string test 
8593                  line_split = line.split() 
8594   
8595                  # Continue for comment lines. 
8596                  if line_split[0] == "#": 
8597                      print(line), 
8598                      continue 
8599   
8600                  # Assign the split of the line. 
8601                  mol_name, res_num, res_name, spin_num, spin_name, val, sd_error = line_split 
8602                  print(mol_name, res_num, res_name, spin_num, spin_name, val, sd_error) 
8603   
8604                  if res_num == '52': 
8605                      # Assert that the value is not None. 
8606                      self.assertNotEqual(val, 'None') 
8607